chlamydia pneumoniae polypeptides are provided. The C. pneumoniae polypeptides can be used to prepare pharmaceutical compositions for the treatment or prevention of disease. In addition, the proteins can be used in methods for the diagnosis of C. pneumoniae infection.
|
1. An isolated chlamydia pneumoniae protein comprising the amino acid sequence set forth in SEQ ID NO: 1047.
3. The composition of
4. The composition of
6. The isolated chlamydia pneumoniae protein of
|
|||||||||||||||||||||||||||||||
The present application is related to No. 60/128,606, filed Apr. 8, 1999 and No. 60/108,279, filed Nov. 12, 1998, which are incorporated herein by reference.
1. Field of the Invention
This invention relates to nucleic acids and polypeptides from Chlamydia pneumoniae and to their use in the diagnosis, prevention and treatment of diseases associated with C. pneumoniae.
2. Background of the Invention
Chlamydiaceae is a family of obligate intracellular parasite with a tropism for epithelial cells lining the mucus membranes. The bacteria have two morphologically distinct forms, "elementary body" and "reticulate body". The elementary body is the infectious form, and has a rigid cell wall, primarily of cross-linked outer membrane proteins. The reticulate body is the intracellular, metabolically active form. A unique developmental cycle between these two forms characterizes Chlamydia growth.
C. pneumoniae is a human respiratory pathogen that causes acute respiratory disease, and approximately 10% of community-acquired pneumonia Antibody prevalence studies have shown that virtually everyone is infected with C. pneumoniae at some time, and that reinfection is common. In addition to respiratory disease, studies have shown an association of this organism with coronary artery disease. It has been demonstrated in atherosclerotic lesions of the aorta and coronary arteries by immunocytochemistry and by polymerase chain reaction (Kuo et al. (1993) J Infect Dis 167(4):841-849).
Recent reports have further demonstrated the presence of C. pneumoniae in the walls of abdominal aortic aneurysms (Juvonen et al. (1997) J Vasc Surg 25(3):499-505). Abdominal aortic aneurysms are frequently associated with atherosclerosis, and inflammation may be an important factor in aneurysmal dilatation. C. pneumoniae may play a role in maintaining an inflammation and triggering the development of aortic aneurysms.
Muhlestein et al. (1996) JACC 27:1555-61, reported a differential incidence of Chlamydia species within the coronary artery wall of patients with atherosclerosis versus those with other forms of cardiovascular disease. The extremely high rate of possible infection in patients with symptomatic atherosclerotic disease compared to the very low rate in patients with normal coronary arteries or coronary artery disease from chronic transplant rejection provides evidence for a direct link between the atherosclerotic process and Chlamydia infection. Because a history of chlamydial infection is so prevalent in the population, the issue of causality remains. On a physiologic and pathologic level, abnormal interactions among endothelial cells, platelets, macrophages and lymphocytes may lead to a cascade of events resulting in acute endothelial damage, thrombosis and repair, chronically leading to the development of atheroma in blood vessels.
C. pneumoniae is related to other Chlamydia species, but the level of sequence similarity is relatively low. Very little is known about the biology of this organism, although it appears to be an important human pathogen. Allelic diversity and structural relationships between specific genes of Chlamydia species is described in Kaltenboeck et al. (1993) J Bacteriol 175(2):487-502; Gaydos et al. (1992) Infect Immun 60(12):5319-5323; Everett et al. (1997) Int J Syst Bacteriol 47(2):461-473; and Pudjiatmoko et al. (1997) Int J Syst Bacteriol 47(2):425-431.
A number of studies have been published describing methods for detection of C. pneumoniae, and for distinguishing between Chlamydia species. Such methods include PCR detection (Rasmussen et al. (1992) Mol Cell Probes 6(5):389-394; Holland et al. (1990) J Infect Dis 162(4):984-987); a simplified polymerase chain reaction-enzyme immunoassay (Wilson et al. (1996) J Appl Bacteriol 80(4):431-438); sequence determination and restriction endonuclease cleavage (Herrmann et al. (1996) J Clin Microbiol 34(8):1897-1902).
Antigenic and molecular analyses of different C. pneumoniae strains is described in Jantos et al. (1997) Clin Microbiol 35(3):620-623. Some genes of C. pneumoniae have been isolated and sequenced. These include the Gro E operon (Kikuta et al. (1991) Infect Immun 59(12):4665-4669); the major outer membrane protein Perez et al. (1991) Infect Immun 59(6):2195-2199; the DnaK protein homolog (Komak et al. (1991) Infect Immun 59(2):721-725); as well as a number of ribosomal and other genes.
This invention provides the genomic sequence of Chlamydia pneumoniae. The sequence information is useful for a variety of diagnostic and analytical methods. The genomic sequence may be embodied in a variety of media, including computer readable forms, or as a nucleic acid comprising a selected fragment of the sequence. Such fragments generally consist of an open reading frame, transcriptional or translational control elements, or fragments derived therefrom. Proteins encoded by the open reading frames are useful for diagnostic purposes, as well as for their enzymatic or structural activity.
The term "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an α carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group., e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
"Amplification" primers are oligonucleotides comprising either natural or analogue nucleotides that can serve as the basis for the amplification of a select nucleic acid sequence. They include, e.g., polymerase chain reaction primers and ligase chain reaction oligonucleotides.
"Antibody" refers to an immunoglobulin molecule able to bind to a specific epitope on an antigen. Antibodies can be a polyclonal mixture or monoclonal. Antibodies can be intact immunoglobulins derived from natural sources or from recombinant sources and can be immunoreactive portions of intact immunoglobulins. Antibodies may exist in a variety of forms including, for example, Fv, Fab, and F(ab)2, as well as in single chains. Single-chain antibodies, in which genes for a heavy chain and a light chain are combined into a single coding sequence, may also be used.
An "antigen" is a molecule that is recognized and bound by an antibody, e.g., peptides, carbohydrates, organic molecules, or more complex molecules such as glycolipids and glycoproteins. The part of the antigen that is the target of antibody binding is an antigenic determinant and a small functional group that corresponds to a single antigenic determinant is called a hapten.
"Biological sample" refers to any sample obtained from a living or dead organism. Examples of biological samples include biological fluids and tissue specimens. Such biological samples can be prepared for analysis of the presence of C. pneumoniae nucleic acids, proteins, or antibodies specifically reactive with the proteins.
The term "C. pneumoniae gene" shall be intended to mean the open reading frame encoding specific C. pneumoniae polypeptides, as well as adjacent 5' and 3' non-coding nucleotide sequences involved in the regulation of expression, up to about 2 kb beyond the coding region, but possibly further in either direction. The gene may be introduced into an appropriate vector for extrachromosomal maintenance or for integration into a host genome.
"Conservatively modified variants" applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acids Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 206:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silen: variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.
As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.
The following groups each contain amino acids that are conservative substitutions for one another:
1) Alanine (A), Glycine (G);
2) Serine (S), Threonine (T);
3) Aspartic acid (D), Glutamic acid (E);
4) Asparagine (N), Glutamine (Q);
5) Cysteine (C), Methionine (M);
6) Arginine (R), Lysine (K), Histidine (H);
7) Isoleucine (I), Leucine (L), Valine (V); and
8) Phenylalanine (F), Tyrosine (Y), Tryptophan (W). see, e.g., Creighton, Proteins (1984)).
The terms "identical" or percent "identity," in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. This definition also refers to the complement of a test sequence, which has a designated percent sequence or subsequence complementarity when the test sequence has a designated or substantial identity to a reference sequence. For example, a designated amino acid percent identity of 95% refers to sequences or subsequences that have at least about 95% amino acid identity when aligned for maximum correspondence over a comparison window as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences would then be said to have substantial identity, or to be substantially identical to each other. Preferably, sequences have at least about 70% identity, more preferably 80% identity, more preferably 90-95% identity and above. Preferably, the percent identity exists over a region of the sequence that is at least about 25 amino acids in length, more preferably over a region that is 50-100 amino acids in length.
When percentage of sequence identity is used in reference to proteins or peptides, it is recognized that residue positions that are not identical often differ by conservative amino acid substitutions, where amino acids residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated according to, e.g., the algorithm of Meyers & Miller, Computer Applic. Biol. Sci. 4:11-17 (1988) e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif., USA).
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated or default program parameters.
A comparison window includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 25 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Ausubel et al., supra).
One example of a useful algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments to show relationship and percent sequence identity. It also plots a tree or dendogram showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351-360 (1987). The method used is similar to the method described by Higgins & Sharp, CABIOS 5:151-153 (1989). The program can align up to 300 sequences, each of a maximum length of 5,000 nucleotides or amino acids. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster is then aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences are aligned by a simple extension of the pairwise alignment of two individual sequences. The final alignment is achieved by a series of progressive, pairwise alignments. The program is run by designating specific sequences and their amino acid or nucleotide coordinates for regions of sequence comparison and by designating the program parameters. Using PILEUP, a reference sequence is compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted end gaps. PILEUP can be obtained from the GCG sequence analysis software package, e.g, version 7.0 (Devereaux et al., Nuc. Acids Res. 12:387-395 (1984).
Another example of algorithm that is suitable for determining percent sequence identity (i.e., substantial similarity or identity) is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues, always<0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as default parameters a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).
The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
An indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below.
Another indication that polynucleotide sequences are substantially identical is if two molecules hybridize to each other under stringent conditions. Stringent conditions are sequence dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5°C C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Typically stringent conditions for a Southern blot protocol involve hybridizing in a buffer comprising 5×SSC, 1% SDS at 65°C C. or hybridizing in a buffer containing 5×SSC and 1% SDS at 42°C C. and washing at 65°C C. with a 0.2×SSC, 0.1% SDS wash.
A "label" is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include 32P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, dioxigenin, or haptens and proteins for which antisera or monoclonal antibodies are available.
The term "nucleic acid" refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).
Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. The term nucleic acid is used interchangeably with gene, cDNA, mRNA oligonucleotide, and polynucleotide.
As used herein a "nucleic acid probe or oligonucleotide" is defined as a nucleic acid capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. As used herein, a probe may include natural (i.e., A, G, C, or T) or modified bases (7-deazaguanosine, inosine, etc.). In addition, the bases in a probe may be joined by a linkage other than a phosphodiester bond, so long as it does not interfere with hybridization. Thus, for example, probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages. It will be understood by one of skill in the art that probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency of the hybridization conditions. The probes are preferably directly labeled as with isotopes, chromophores, lumiphores, chromogens, or indirectly labeled such as with biotin to which a streptavidin complex may later bind. By assaying for the presence or absence of the probe, one can detect the presence or absence of the select sequence or subsequence.
A labeled nucleic acid probe or oligonucleotide is one that is bound, either covalently, through a linker, or through ionic, van der Waals or hydrogen bonds to a label such that the presence of the probe may be detected by detecting the presence of the label bound to the probe.
"Pharmaceutically acceptable" means a material that is not biologically or otherwise undesirable, i.e., the material can be administered to an individual along with a Chlamydia antigen without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition.
The terms "polypeptide," "peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an analog or mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers.
The phrase "specifically or selectively hybridizing to," refers to hybridization between a probe and a target sequence in which the probe binds substantially only to the target sequence, forming a hybridization complex, when the target is in a heterogeneous mixture of polynucleotides and other compounds. Such hybridization is determinative of the presence of the target sequence. Although the probe may bind other unrelated sequences, at least 90%, preferably 95% or more of the hybridization complexes formed are with the target sequence.
The term "recombinant" when used with reference to a cell, or nucleic acid, or vector, indicates that the cell, or nucleic acid, or vector, has been modified by the introduction of a heterologous nucleic acid or the alteration of a native nucleic acid, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all.
The phrase "specifically immunoreactive with", when referring to a protein or peptide, refers to a binding reaction between the protein and an antibody which is determinative of the presence of the protein in the presence of a heterogeneous population of proteins and other compounds. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein and do not bind in a significant amount to other proteins present in the sample. Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein and are described in detail below.
The phrase "substantially pure" or "isolated" when referring to a Chlamydia peptide or protein, means a chemical composition which is free of other subcellular components of the Chlamydia organism. Typically, a monomeric protein is substantially pure when at least about 85% or more of a sample exhibits a single polypeptide backbone. Minor variants or chemical modifications may typically share the same polypeptide sequence. Depending on the purification procedure, purities of 85%, and preferably over 95% pure are possible. Protein purity or homogeneity may be indicated by a number of means well known in the art, such as polyacrylamide gel electrophoresis of a protein sample, followed by visualizing a single polypeptide band on a polyacrylamide gel upon silver staining. For certain purposes high resolution will be needed and HPLC or a similar means for purification utilized.
The present invention provides the nucleotide sequence of the C. pneumoniae genome SEQ ID NO: 1 or a representative fragment thereof, in a form which can be readily used, analyzed, and interpreted by a skilled artisan. As used herein, a "representative fragment" of the nucleotide sequence depicted in SEQ ID NO: 1 refers to any portion which is not presently represented within a publicly available database. Preferred representative fragments of the present invention are open reading frames, expression modulating fragments, uptake modulating fragments, and fragments which can be used to diagnose the presence of C. pneumoniae in sample. Using the information provided in the present application, together with routine cloning and sequencing methods, one of ordinary skill in the art will be able to clone and sequence all "representative fragments" of interest including open reading frames (ORFs) encoding a large variety of C. pneumoniae proteins. A non-limiting identification of such preferred representative fragments is provided in Table 2 (see Sequence Listing, SEQ ID NOS:2-1074).
Diagnostic use of C. pneumoniae Nucleic Acids
Hybridization-based Assays
Using the nucleic acids disclosed here, one of skill can design nucleic acid hybridization-based assays for the detection of C. pneumoniae. Any of a number of well known techniques for the specific detection of target nucleic acids can be used. Exemplary hybridization-based assays include, but are not limited to, traditional "direct probe" methods such as Southern Blots, dot blots, in situ hybridization (e.g., FISH), PCR, and the like. The methods can be used in a wide variety of formats including, but not limited to substrate-(e.g. membrane or glass) bound methods or array-based approaches as described below. As noted above, this invention also embraces methods for detecting the presence of Chlamydia DNA or RNA in biological samples. These sequences can be used to detect Chlamydia in biological samples from patients suspected of being infected. A variety of methods of specific DNA and RNA measurement using nucleic acid hybridization techniques are known to those of skill in the art (see Sambrook et al., supra).
In situ hybridization assays are well known (e.g., Angerer (1987) Meth. Enzymol 152: 649). Generally, in situ hybridization comprises the following major steps: (1) fixation of tissue or biological structure to analyzed; (2) prehybridization treatment of the biological structure to increase accessibility of target DNA, and to reduce nonspecific binding; (3) hybridization of the mixture of nucleic acids to the nucleic acid in the biological structure or tissue; (4) post-hybridization washes to remove nucleic acid fragments not bound in the hybridization and (5) detection of the hybridized nucleic acid fragments. The reagent used in each of these steps and the conditions for use vary depending on the particular application.
In a typical in situ hybridization assay, cells are fixed to a solid support, typically a glass slide. If a nucleic acid is to be probed, the cells are typically denatured with heat or alkali. The cells are then contacted with a hybridization solution at a moderate temperature to permit annealing of labeled probes specific to the nucleic acid sequence encoding the protein. The targets (e.g., cells) are then typically washed at a predetermined stringency or at an increasing stringency until an appropriate signal to noise ratio is obtained.
The nucleic acids of this invention are particularly well suited to array-based hybridization formats. Arrays are a multiplicity of different "probe" or "target" nucleic acids (or other compounds) attached to one or more surfaces (e.g., solid, membrane, or gel). In a preferred embodiment, the multiplicity of nucleic acids (or other moieties) is attached to a single contiguous surface or to a multiplicity of surfaces juxtaposed to each other.
In an array format a large number of different hybridization reactions can be run essentially "in parallel." This provides rapid, essentially simultaneous, evaluation of a number of hybridizations in a single "experiment". Methods of performing hybridization reactions in array based formats are well known to those of skill in the art (see, e.g., Pastinen (1997) Genome Res. 7: 606-614; Jackson (1996) Nature Biotechnology 14:1685; Chee (1995) Science 274: 610; WO 96/17958.
Arrays, particularly nucleic acid arrays can be produced according to a wide variety of methods well known to those of skill in the art. For example, in a simple embodiment, "low density" arrays can simply be produced by spotting (e.g. by hand using a pipette) different nucleic acids at different locations on a solid support (e.g. a glass surface, a membrane, etc.).
This simple spotting, approach has been automated to produce high density spotted arrays (see, e.g., U.S. Pat. No. 5,807,522). This patent describes the use of an automated systems that taps a microcapillary against a surface to deposit a small volume of a biological sample. The process is repeated to generate high density arrays. Arrays can also be produced using oligonucleotide synthesis technology. Thus, for example, U.S. Pat. No. 5,143,854 and PCT patent publication Nos. WO 90/15070 and 92/10092 teach the use of light-directed combinatorial synthesis of high density oligonucleotide arrays.
Many methods for immobilizing nucleic acids on a variety of solid surfaces are known in the art. A wide variety of organic and inorganic polymers, as well as other materials, both natural and synthetic, can be employed as the material for the solid surface. Illustrative solid surfaces include, e.g., nitrocellulose, nylon, glass, quartz, diazotized membranes (paper or nylon), silicones, polyformaldehyde, cellulose, and cellulose acetate. In addition, plastics such as polyethylene, polypropylene, polystyrene, and the like can be used. Other materials which may be employed include paper, ceramics, metals, metalloids, semiconductive materials, cermets or the like. In addition, substances that form gels can be used. Such materials include, e.g., proteins (e.g., gelatins), lipopolysaccharides, silicates, agarose and polyacrylamides. Where the solid surface is porous, various pore sizes may be employed depending upon the nature of the system.
In preparing the surface, a plurality of different materials may be employed, particularly as laminates, to obtain various properties. For example, proteins (e.g., bovine serum albumin) or mixtures of macromolecules (e.g., Denhardt's solution) can be employed to avoid non-specific binding, simplify covalent conjugation, enhance signal detection or the like. If covalent bonding between a compound and the surface is desired, the surface will usually be polyfunctional or be capable of being polyfunctionalized. Functional groups which may be present on the surface and used for linking can include carboxylic acids, aldehydes, amino groups, cyano groups, ethylenic groups, hydroxyl groups, mercapto groups and the like. The manner of linking a wide variety of compounds to various surfaces is well known and is amply illustrated in the literature.
For example, methods for immobilizing nucleic acids by introduction of various functional groups to the molecules is known (see, e.g., Bischoff (1987) Anal. Biochem., 164: 336-344; Kremsky (1987) Nucl. Acids Res. 15: 2891-2910). Modified nucleotides can be placed on the target using PCR primers containing the modified nucleotide, or by enzymatic end labeling with modified nucleotides. Use of glass or membrane supports (e.g., nitrocellulose, nylon, polypropylene) for the nucleic acid arrays of the invention is advantageous because of well developed technology employing manual and robotic methods of arraying targets at relatively high element densities. Such membranes are generally available and protocols and equipment for hybridization to membranes is well known.
Target elements of various sizes, ranging from 1 mm diameter down to 1 μm can be used. Smaller target elements containing low amounts of concentrated, fixed probe DNA are used for high complexity comparative hybridizations since the total amount of sample available for binding to each target element will be limited. Thus it is advantageous to have small array target elements that contain a small amount of concentrated probe DNA so that the signal that is obtained is highly localized and bright. Such small array target elements are typically used in arrays with densities greater than 104/cm2. Relatively simple approaches capable of quantitative fluorescent imaging of 1 cm2 areas have been described that permit acquisition of data from a large number of target elements in a single image (see, e.g., Wittrup (1994) Cytometry 16:206-213).
If fluorescently labeled nucleic acid samples are used, arrays on solid surface substrates with much lower fluorescence than membranes, such as glass, quartz, or small beads, can achieve much better sensitivity. Substrates such as glass or fused silica are advantageous in that they provide a very low fluorescence substrate, and a highly efficient hybridization environment. Covalent attachment of the target nucleic acids to glass or synthetic fused silica can be accomplished according to a number of known techniques (described above). Nucleic acids can be conveniently coupled to glass using commercially available reagents. For instance, materials for preparation of silanized glass with a number of functional groups are commercially available or can be prepared using standard techniques (see, e.g., Gait (1984) Oligonucleotide Synthesis: A Practical Approach, IRL Press, Wash., D.C.). Quartz cover slips, which have at least 10-fold lower autofluorescence than glass, can also be silanized.
Alternatively, probes can also be immobilized on commercially available coated beads or other surfaces. For instance, biotin end-labeled nucleic acids can be bound to commercially available avidin-coated beads. Streptavidin or anti-digoxigenin antibody can also be attached to silanized glass slides by protein-mediated coupling using e.g., protein A following standard protocols (see, e.g., Smith (1992) Science 258: 1122-1126). Biotin or digoxigenin end-labeled nucleic acids can be prepared according to standard techniques. Hybridization to nucleic acids attached to beads is accomplished by suspending them in the hybridization mix, and then depositing them on the glass substrate for analysis after washing. Alternatively, paramagnetic particles, such as ferric oxide particles, with or without avidin coating, can be used.
A variety of other nucleic acid hybridization formats are known to those skilled in the art. For example, common formats include sandwich assays and competition or displacement assays. Hybridization techniques are generally described in Hames and Higgins (1985) Nucleic Acid Hybridization, A Practical Approach, IRL Press; Gall and Pardue (1969) Proc. Natl. Acad. Sci. USA 63: 378-383; and John et al. (1969) Nature 223: 582-587.
Sandwich assays are commercially useful hybridization assays for detecting or isolating nucleic acid sequences. Such assays utilize a "capture" nucleic acid covalently immobilized to a solid support and a labeled "signal" nucleic acid in solution. The sample will provide the target nucleic acid. The "capture" nucleic acid and "signal" nucleic acid probe hybridize with the target nucleic acid to form a "sandwich" hybridization complex. To be most effective, the signal nucleic acid should not hybridize with the capture nucleic acid.
Detection of a hybridization complex may require the binding of a signal generating complex to a duplex of target and probe polynucleotides or nucleic acids. Typically, such binding occurs through ligand and anti-ligand interactions as between a ligand-conjugated probe and an anti-ligand conjugated with a signal.
The sensitivity of the hybridization assays may be enhanced through use of a nucleic acid amplification system that multiplies the target nucleic acid being detected. Examples of such systems include the polymerase chain reaction (PCR) system and the ligase chain reaction (LCR) system. Other methods recently described in the art are the nucleic acid sequence based amplification (NASBAO, Cangene, Mississauga, Ontario) and Q Beta Replicase systems.
Nucleic acid hybridization simply involves providing a denatured probe and target nucleic acid under conditions where the probe and its complementary target can form stable hybrid duplexes through complementary base pairing. The nucleic acids that do not form hybrid duplexes are then washed away leaving the hybridized nucleic acids to be detected, typically through detection of an attached detectable label. It is generally recognized that nucleic acids are denatured by increasing the temperature or decreasing the salt concentration of the buffer containing the nucleic acids, or in the addition of chemical agents, or the raising of the pH. Under low stringency conditions (e.g., low temperature and/or high salt and/or high target concentration) hybrid duplexes (e.g., DNA:DNA, RNA:RNA, or RNA:DNA) will form even where the annealed sequences are not perfectly complementary. Thus specificity of hybridization is reduced at lower stringency. Conversely, at higher stringency (e.g., higher temperature or lower salt) successful hybridization requires fewer mismatches.
One of skill in the art will appreciate that hybridization conditions may be selected to provide any degree of stringency. In a preferred embodiment, hybridization is performed at low stringency to ensure hybridization and then subsequent washes are performed at higher stringency to eliminate mismatched hybrid duplexes. Successive washes may be performed at increasingly higher stringency (e.g., down to as low as 0.25×SSPE-T at 37°C C. to 70°C C.) until a desired level of hybridization specificity is obtained. Stringency can also be increased by addition of agents such as formamide. Hybridization specificity may be evaluated by comparison of hybridization to the test probes with hybridization to the various controls that can be present.
In general, there is a tradeoff between hybridization specificity (stringency) and signal intensity. Thus, in a preferred embodiment, the wash is performed at the highest stringency that produces consistent results and that provides a signal intensity greater than approximately 10% of the background intensity. Thus, in a preferred embodiment, the hybridized array may be washed at successively higher stringency solutions and read between each wash. Analysis of the data sets thus produced will reveal a wash stringency above which the hybridization pattern is not appreciably altered and which provides adequate signal for the particular probes of interest.
Methods of optimizing hybridization conditions are well known to those of skill in the art (see, eg., Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24: Hybridization With Nucleic Acid Probes, Elsevier, N.Y.).
Labeling and Detection of Nucleic Acids
In a preferred embodiment, the hybridized nucleic acids are detected by detecting one or more labels attached to the sample or probe nucleic acids. The labels may be incorporated by any of a number of means well known to those of skill in the art. Means of attaching labels to nucleic acids include, for example nick translation to end-labeling (e.g. with a labeled RNA) by kinasing of the nucleic acid and subsequent attachment (ligation) of a nucleic acid linker joining the sample nucleic acid to a label (e.g., a fluorophore). A wide variety of linkers for the attachment of labels to nucleic acids are also known. In addition, intercalating dyes and fluorescent nucleotides can also be used.
Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein, texas red, rhodamine, green fluorescent protein, and the like, see, e.g., Molecular Probes, Eugene, Oreg., USA), radiolabels (e.g., 3H, 125I, 35S, 14C, or 32P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold (e.g., gold particles in the 40-80 nm diameter size range scatter green light with high efficiency) or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads. Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241.
A fluorescent label is preferred because it provides a very strong signal with low background. It is also optically detectable at high resolution and sensitivity through a quick scanning procedure. The nucleic acid samples can all be labeled with a single label, e.g., a single fluorescent label. Alternatively, in another embodiment, different nucleic acid samples can be simultaneously hybridized where each nucleic acid sample has a different label. For instance, one target could have a green fluorescent label and a second target could have a red fluorescent label. The scanning step will distinguish cites of binding of the red label from those binding the green fluorescent label. Each nucleic acid sample (target nucleic acid) can be analyzed independently from one another.
Suitable chromogens which can be employed include those molecules and compounds which absorb light in a distinctive range of wavelengths so that a color can be observed or, alternatively, which emit light when irradiated with radiation of a particular wave length or wave length range, e.g., fluorescers.
Desirably, fluorescers should absorb light above about 300 nm, preferably about 350 nm, and more preferably above about 400 nm, usually emitting at wavelengths greater than about 10 nm higher than the wavelength of the light absorbed. It should be noted that the absorption and emission characteristics of the bound dye can differ from the unbound dye. Therefore, when referring to the various wavelength ranges and characteristics of the dyes, it is intended to indicate the dyes as employed and not the dye which is unconjugated and characterized in an arbitrary solvent.
Fluorescers are generally preferred because by irradiating a fluorescer with light, one can obtain a plurality of emissions. Thus, a single label can provide for a plurality of measurable events.
Detectable signal can also be provided by chemiluminescent and bioluminescent sources. Chemiluminescent sources include a compound which becomes electronically excited by a chemical reaction and can then emit light which serves as the detectable signal or donates energy to a fluorescent acceptor. Alternatively, luciferins can be used in conjunction with luciferase or lucigenins to provide bioluminescence. Spin labels are provided by reporter molecules with an unpaired electron spin which can be detected by electron spin resonance (ESR) spectroscopy. Exemplary spin labels include organic free radicals, transitional metal complexes, particularly vanadium, copper, iron, and manganese, and the like. Exemplary spin labels include nitroxide free radicals.
The label may be added to the target (sample) nucleic acid(s) prior to, or after the hybridization. So called "direct labels" are detectable labels that are directly attached to or incorporated into the target (sample) nucleic acid prior to hybridization. In contrast, so called "indirect labels" are joined to the hybrid duplex after hybridization. Often, the indirect label is attached to a binding moiety that has been attached to the target nucleic acid prior to the hybridization. Thus, for example, the target nucleic acid may be biotinylated before the hybridization. After hybridization, an avidin-conjugated fluorophore will bind the biotin bearing hybrid duplexes providing a label that is easily detected. For a detailed review of methods of labeling nucleic acids and detecting labeled hybridized nucleic acids see Laboratory Techniques in Biochemistry and Molecular Biology; Vol. 24: Hybridization With Nucleic Acid Probes, P. Tijssen, ed. Elsevier, N.Y., (1993)).
Fluorescent labels are easily added during an in vitro transcription reaction. Thus, for example, fluorescein labeled UTP and CTP can be incorporated into the RNA produced in an in vitro transcription.
The labels can be attached directly or through a linker moiety. In general, the site of label or linker-label attachment is not limited to any specific position. For example, a label may be attached to a nucleoside, nucleotide, or analogue thereof at any position that does not interfere with detection or hybridization as desired. For example, certain Label-ON Reagents from Clontech (Palo Alto, Calif.) provide for labeling interspersed throughout the phosphate backbone of an oligonucleotide and for terminal labeling at the 3' and 5' ends. As shown for example herein, labels can be attached at positions on the ribose ring or the ribose can be modified and even eliminated as desired. The base moieties of useful labeling reagents can include those that are naturally occurring or modified in a manner that does not interfere with the purpose to which they are put. Modified bases include but are not limited to 7-deaza A and G, 7-deaza-8-aza A and G, and other heterocyclic moieties.
It will be recognized that fluorescent labels are not to be limited to single species organic molecules, but include inorganic molecules, multi-molecular mixtures of organic and/or inorganic molecules, crystals, heteropolymers, and the like. Thus, for example, CdSe-CdS core-shell nanocrystals enclosed in a silica shell can be easily derivatized for coupling to a biological molecule (Bruchez et al (1998) Science, 281: 2013-2016). Similarly, highly fluorescent quantum dots (zinc sulfide-capped cadmium selenide) have been covalently coupled to biomolecules for use in ultrasensitive biological detection (Warren and Nie (1998) Science, 281: 2016-2018).
Amplification-based Assays
In another embodiment, amplification-based assays can be used to detect nucleic acids. In such amplification-based assays, the nucleic acid sequences act as a template in an amplification reaction (e.g. Polymerase Chain Reaction (PCR). Detailed protocols for quantitative PCR are provided in Innis et al. (1990) PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc. N.Y.).
Other suitable amplification methods include, but are not limited to ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4: 560, Landegren et al. (1988) Science 241: 1077, and Barringer et al. (1990) Gene 89: 117, transcription amplification (Kwoh et al (1989) Proc. Natl. Acad. Sci. USA 86: 1173), and self-sustained sequence replication (Guatelli et al. (1990) Proc. Nat. Acad. Sci. USA 87: 1874).
Detection of C. pneumoniae Gene Expression
The nucleic acids of the invention can also be used to C. pneumoniae detect gene transcripts. Methods of detecting and/or quantifying gene transcripts using nucleic acid hybridization techniques are known to those of skill in the art (see Sambrook et al. supra). For example, a Northern transfer may be used for the detection of the desired mRNA directly. In brief, the mRNA is isolated from a given cell sample using, for example, an acid guanidinium-phenol-chloroform extraction method. The mRNA is then electrophoresed to separate the mRNA species and the mRNA is transferred from the gel to a nitrocellulose membrane. As with the Southern blots, labeled probes are used to identify and/or quantify the target mRNA.
In another preferred embodiment, the gene transcript can be measured using amplification (e.g. PCR) based methods as described above for directly assessing copy number of the target sequences.
Expression of C. pneumoniae Proteins
The nucleic acids disclosed here can be used for recombinant expression of the proteins. In these methods, the nucleic acids encoding the proteins of interest are introduced into suitable host cells, followed by induction of the cells to produce large amounts of the protein. The invention relies on routine techniques in the field of disclosing the general methods of use in this invention is Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed. 1989).
Standard transfection methods are used to produce prokaryotic, mammalian, yeast or insect cell lines which express large quantities of the desired polypeptide, which is then purified using standard techniques (see. e.g., Colley et al., J. Biol. Chem. 264:17619-17622, 1989; Guide to Protein Purification, supra).
The nucleotide sequences used to transfect the host cells can be modified to yield Chlamydia polypeptides with a variety of desired properties. For example, the polypeptides can vary from the naturally-occurring sequence at the primary structure level by amino acid, insertions, substitutions, deletions, and the like. These modifications can be used in a number of combinations to produce the final modified protein chain.
The amino acid sequence variants can be prepared with various objectives in mind, including facilitating purification and preparation of the recombinant polypeptide. The modified polypeptides are also useful for modifying plasma half life, improving therapeutic efficacy, and lessening the severity or occurrence of side effects during therapeutic use. The amino acid sequence variants are usually predetermined variants not found in nature but exhibit the same immunogenic activity as naturally occurring protein. In general, modifications of the sequences encoding the polypeptides may be readily accomplished by a variety of well-known techniques, such as site-directed mutagenesis (see Gillman & Smith, Gene 8:81-97 (1979); Roberts et al., Nature 328:731-734 (1987)). One of ordinary skill will appreciate that the effect of many mutations is difficult to predict. Thus, most modifications are evaluated by routine screening in a suitable assay for the desired characteristic. For instance, the effect of various modifications on the ability of the polypeptide to elicit a protective immune response can be easily determined using in vitro assays. For instance, the polypeptides can be tested for their ability to induce lymphoproliferation, T cell cytotoxicity, or cytokine production using standard techniques.
The particular procedure used to introduce the genetic material into the host cell for expression of the polypeptide is not particularly critical. Any of the well known procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, spheroplasts, electroporation, liposomes, microinjection, plasmid vectors, viral vectors and any of the other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see Sambrook et al., supra). It is only necessary that the particular procedure utilized be capable of successfully introducing at least one gene into the host cell which is capable of expressing the gene.
Any of a number of well known cells and cell lines can be used to express the polypeptides of the invention. For instance, prokaryotic cells such as E. coli can be used. Eukaryotic cells include, yeast, Chinese hamster ovary (CHO) cells, COS cells, and insect cells.
The particular vector used to transport the genetic information into the cell is also not particularly critical. Any of the conventional vectors used for expression of recombinant proteins in prokaryotic and eukaryotic cells may be used. Expression vectors for mammalian cells typically contain regulatory elements from eukaryotic viruses.
The expression vector typically contains a transcription unit or expression cassette that contains all the elements required for the expression of the polypeptide DNA in the host cells. A typical expression cassette contains a promoter operably linked to the DNA sequence encoding a polypeptide and signals required for efficient polyadenylation of the transcript. The term "operably linked" as used herein refers to linkage of a promoter upstream from a DNA sequence such that the promoter mediates transcription of the DNA sequence. The promoter is preferably positioned about the same distance from the heterologous transcription start site as it is from the transcription start site in its natural setting. As is known in the art, however, some variation in this distance can be accommodated without loss of promoter function.
Following the growth of the recombinant cells and expression of the polypeptide, the culture medium is harvested for purification of the secreted protein. The media are typically clarified by centrifugation or filtration to remove cells and cell debris and the proteins are concentrated by adsorption to any suitable resin or by use of ammonium sulfate fractionation, polyethylene glycol precipitation, or by ultrafiltration. Other routine means known in the art may be equally suitable. Further purification of the polypeptide can be accomplished by standard techniques, for example, affinity chromatography, ion exchange chromatography, sizing chromatography, His6 tagging and Ni-agarose chromatography (as described in Dobeli et al., Mol. and Biochem. Parasit. 41:259-268 (1990)), or other protein purification techniques to obtain homogeneity. The purified proteins are then used to produce pharmaceutical compositions, as described below.
An alternative method of preparing recombinant polypeptides useful as vaccines involves the use of recombinant viruses (e.g., vaccinia). Vaccinia virus is grown in suitable cultured mammalian cells such as the HeLa S3 spinner cells, as described by Mackett et al., in DNA cloning Vol. II: A practical approach, pp. 191-211 (Glover, ed.).
Antibody Production
The proteins of the present invention can be used to produce antibodies specifically reactive with C pneumoniae antigens. If isolated proteins are used, they may be recombinantly produced or isolated from Chlamydia cultures. Synthetic peptides made using the protein sequences may also be used.
Methods of production of polyclonal antibodies are known to those of skill in the art. In brief, an immunogen, preferably a purified protein, is mixed with an adjuvant and animals are immunized. When appropriately high titers of antibody to the immunogen are obtained, blood is collected from the animal and antisera is prepared. Further fractionation of the antisera to enrich for antibodies reactive to Chlamydia proteins can be done if desired (see Harlow & Lane, Antibodies: A Laboratory Manual (1988)).
Polyclonal antisera are used to identify and characterize Chlamydia in the tissues of patients using, for instance, in situ techniques and immunoperoxidase test procedures described in Anderson et al. JAVMA 198:241 (1991) and Barr et al. Vet. Pathol. 28:110-116 (1991).
Monoclonal antibodies may be obtained by various techniques familiar to those skilled in the art. Briefly, spleen cells from an animal immunized with a desired antigen are immortalized, commonly by fusion with a myeloma cell (see Kohler & Milstein, Eur. J. Immunol. 6:511-519(1976)). Alternative methods of immortalization include transformation with Epstein Barr Virus, oncogenes, or retroviruses, or other methods well known in the art. Colonies arising from single immortalized cells are screened for production of antibodies of the desired specificity and affinity for the antigen, and yield of the monoclonal antibodies produced by such cells may be enhanced by various techniques, including injection into the peritoneal cavity of a vertebrate host.
Monoclonal antibodies produced in such a manner are used, for instance, in ELISA diagnostic tests, immunoperoxidase tests, immunohistochemical tests, for the in vitro evaluation of spirochete invasion, to select candidate antigens for vaccine development, protein isolation, and for screening genomic and cDNA libraries to select appropriate gene sequences.
Immunodiagonostic Detection of C. pneumoniae Infections
The present invention also provides methods for detecting the presence or absence of C. pneumoniae, or antibodies reactive with it, in a biological sample. For instance, antibodies specifically reactive with Chlamydia can be detected using either Chlamydia proteins or the isolates described here. The proteins and isolates can also be used to raise specific antibodies (either monoclonal or polyclonal) to detect the antigen in a sample. In addition, the nucleic acids disclosed and claimed here can be used to detect Chlamydia-specific sequences using standard hybridization techniques.
For a review of immunological and immunoassay procedures in general, see Basic and Clinical Immunology (Stites & Terr ed., 7th ed. 1991)). The immunoassays of the present invention can be performed in any of several configurations, which are reviewed extensively in Enzyme Immunoassay (Maggio, ed., 1980); Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology (1985)). For instance, the proteins and antibodies disclosed here are conveniently used in ELISA, immunoblot analysis and agglutination assays.
In brief, immunoassays to measure anti-Chlamydia antibodies or antigens can be either competitive or noncompetitive binding assays. In competitive binding assays, the sample analyte (e.g., anti-Chlamydia antibodies) competes with a labeled analyte (e.g., anti-Chlamydia monoclonal antibody) for specific binding sites on a capture agent (e.g., isolated Chlamydia protein) bound to a solid surface. The concentration of labeled analyte bound to the capture agent is inversely proportional to the amount of free analyte present in the sample.
Noncompetitive assays are typically sandwich assays, in which the sample analyte is bound between two analyte-specific binding reagents. One of the binding agents is used as a capture agent and is bound to a solid surface. The second binding agent is labelled and is used to measure or detect the resultant complex by visual or instrument means.
A number of combinations of capture agent and labelled binding agent can be used. For instance, an isolated Chlamydia protein or culture can be used as the capture agent and labelled anti-human antibodies specific for the constant region of human antibodies can be used as the labelled binding agent. Goat, sheep and other non-human antibodies specific for human immunoglobulin constant regions (e.g., γ or μ) are well known in the art. Alternatively, the anti-human antibodies can be the capture agent and the antigen can be labelled.
Various components of the assay, including the antigen, anti-Chlamydia antibody, or anti-human antibody, may be bound to a solid surface. Many methods for immobilizing biomolecules to a variety of solid surfaces are known in the art. For instance, the solid surface may be a membrane (e.g., nitrocellulose), a microtiter dish (e.g., PVC or polystyrene) or a bead. The desired component may be covalently bound or noncovalently attached through nonspecific bonding.
Alternatively, the immunoassay may be carried out in liquid phase and a variety of separation methods may be employed to separate the bound labeled component from the unbound labelled components. These methods are known to those of skill in the art and include immunoprecipitation, column chromatography, adsorption, addition of magnetizable particles coated with a binding agent and other similar procedures.
An immunoassay may also be carried out in liquid phase without a separation procedure. Various homogeneous immunoassay methods are now being applied to immunoassays for protein analytes. In these methods, the binding of the binding agent to the analyte causes a change in the signal emitted by the label, so that binding may be measured without separating the bound from the unbound labelled component.
Western blot (immunoblot) analysis can also be used to detect the presence of antibodies to Chlamydia in the sample. This technique is a reliable method for confirming the presence of antibodies against a particular protein in the sample. The technique generally comprises separating proteins by gel electrophoresis on the basis of molecular weight, transferring the separated proteins to a suitable solid support, (such as a nitrocellulose filter, a nylon filter, or derivatized nylon filter), and incubating the sample with the separated proteins. This causes specific target antibodies present in the sample to bind their respective proteins. Target antibodies are then detected using labeled anti-human antibodies.
The immunoassay formats described above employ labelled assay components. The label may be coupled directly or indirectly to the desired component of the assay according to methods well known in the art. A wide variety of labels may be used. The component may be labelled by any one of several methods. Traditionally a radioactive label incorporating 3H, 125I, 35S, 14C, or 32P was used. Non-radioactive labels include ligands which bind to labelled antibodies, fluorophores, chemiluminescent agents, enzymes, and antibodies which can serve as specific binding pair members for a labelled ligand. The choice of label depends on sensitivity required, ease of conjugation with the compound, stability requirements, and available instrumentation.
Enzymes of interest as labels will primarily be hydrolases, particularly phosphatases, esterases and glycosidases, or oxidoreductases, particularly peroxidases. Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc. Chemiluminescent compounds include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol. For a review of various labelling or signal producing systems which may be used, see U.S. Pat. No. 4,391,904, which is incorporated herein by reference.
Non-radioactive labels are often attached by indirect means. Generally, a ligand molecule (e.g., biotin) is covalently bound to the molecule. The ligand then binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently detectable or covalently bound to a signal system, such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound. A number of ligands and anti-ligands can be used. Where a ligand has a natural anti-ligand, for example, biotin, thyroxine, and cortisol, it can be used in conjunction with the labelled, naturally occurring anti-ligands. Alternatively, any haptenic or antigenic compound can be used in combination with an antibody.
Some assay formats do not require the use of labelled components. For instance, agglutination assays can be used to detect the presence of the target antibodies. In this case, antigen-coated particles are agglutinated by samples comprising the target antibodies. In this format, none of the components need be labelled and the presence of the target antibody is detected by simple visual inspection.
Pharmaceutical Compositions
The peptides or antibodies (typically monoclonal antibodies) of the present invention and pharmaceutical compositions thereof are useful for administration to mammals, particularly humans, to treat and/or prevent Chlamydia infections. Suitable formulations are found in Remington's Pharmaceutical Sciences, Mack Publishing Company, Philadelphia, Pa., 17th ed. (1985).
The immunogenic peptides or antibodies of the invention are administered prophylactically or to an individual already suffering from the disease. The peptide compositions are administered to a patient in an amount sufficient to elicit an effective immune response to Chlamydia. An effective immune response is one that inhibits infection. An amount adequate to accomplish this is defined as "therapeutically effective dose" or "immunogenically effective dose." Amounts effective for this use will depend on, e.g., the peptide composition, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician, but generally range for the initial immunization (that is for therapeutic or prophylactic administration) from about 0.1 mg to about 1.0 mg per 70 kilogram patient, more commonly from about 0.5 mg to about 0.75 mg per 70 kg of body weight. Boosting dosages are typically from about 0.1 mg to about 0.5 mg of peptide using a boosting regimen over weeks to months depending upon the patient's response and condition. A suitable protocol would include injection at time 0, 4, 2, 6, 10 and 14 weeks, followed by further booster injections at 24 and 28 weeks.
For therapeutic use, administration should begin at the first sign of infection. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. In some circumstances, loading doses followed by boosting doses may be required. The resulting immune response helps to cure or at least partially arrest symptoms and/or complications. Vaccine compositions containing the peptides are administered prophylactically to a patient susceptible to or otherwise at risk of the infection.
The pharmaceutical compositions (containing either peptides or antibodies) are intended for parenteral or oral administration. Preferably, the pharmaceutical compositions are administered parenterally, e.g., subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic polypeptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier. A variety of aqueous carriers may be used, e.g., water, buffered water, 0.4% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.
The compositions may also comprise carriers to enhance the immune response. Useful carriers are well known in the art, and include, e.g., KLH, thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly(lysine:glutamic acid), influenza, hepatitis B virus core protein, hepatitis B virus recombinant vaccine and the like.
For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.
As noted above, the peptide compositions are intended to induce an immune response to Chlamydia. Thus, compositions and methods of administration suitable for maximizing the immune response are preferred. For instance, peptides may be introduced into a host, including humans, linked to a carrier or as a homopolymer or heteropolymer of active peptide units from various Chlamydia proteins disclosed here. Alternatively, a "cocktail" of polypeptides can be used. A mixture of more than one polypeptide has the advantage of increased immunological reaction and, where different peptides are used to make up the polymer, the additional ability to induce antibodies to a number of epitopes.
The compositions also include an adjuvant. As used here, number of adjuvants are well known to one skilled in the art. Suitable adjuvants include incomplete Freund's adjuvant, alum, aluminum phosphate, aluminum hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-Lalanyl-D-isoglutaminyl-L-alanine-2-(1'-2'-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion. The effectiveness of an adjuvant may be determined by measuring the amount of antibodies directed against the immunogenic peptide.
The concentration of immunogenic peptides of the invention in the pharmaceutical formulations can vary widely, i.e. from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.
The peptides of the invention can also be expressed by attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into a host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits an immune response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al. (Nature 351:456-460 (1991)). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g., Salmonella typhi vectors and the like, will be apparent to those skilled in the art from the description herein.
The DNA encoding one or more of the peptides of the invention can also be administered to the patient. This approach is described, for instance, in Wolff et, al., Science 247: 1465-1468 (1990) as well as U.S. Pat. Nos. 5,580,859 and 5,589,466.
In order to enhance serum half-life, the peptides may also be encapsulated, introduced into the lumen of liposomes, prepared as a colloid, or other conventional techniques may be employed which provide an extended serum half-life of the peptides. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), U.S. Pat. Nos. 4, 235,871, 4,501,728 and 4,837,028.
The following examples are offered to illustrate, but no to limit the claimed invention.
This example describes comparison of the C. pneumoniae genome disclosed here and the, previously sequenced, C. trachomatis genome (Stephens, et al. Science 282:754-759 (1998)).
The apparent low level of DNA homology between C. trachomatis and C. pneumoniae (Campbell, et al., J. Clin. Microbiol. 25:1911-1916 (1987)) yet analogous cell structures and developmental cycles, predicts that comparative analysis of the two genomes will significantly enhance the understanding of both pathogens. Identification of genes that are present in one species but not the other are of particular importance for the mutually exclusive biological, virulence and pathogenesis capabilities of each. Identification of genes shared between the two species strongly supports the requirement for these capabilities in a biological system that has, over its long-term association with mammalian host cells, evolved to reduce the metabolic capacities while optimizing survival, growth and transmission of these unique pathogens.
The previously sequenced C. trachomatis genome contains 1,042,519 nucleotides and 875 likely protein-coding genes. Similarity searching permitted the inferred functional assignment of sequences 636 (60%) genes disclosedlhere and 251 (23%) are similar to hypothetical genes for other bacterial organisms including those for C. trachomatis. The remaining 186 (17%) genes are not homologous to sequences deposited in GenBank., Seventy C. trachomatis genes are not represented in the C. pneumoniae genome. These are contained within blocks consisting of 2-17 genes and 19 single genes. Of the 70 C. trachomatis genes without homologs in C. pneumoniae, 60 are classified as encoding hypothetical proteins. The remaining genes not represented in C. pneumoniae consist of the tryptophan operon (trpA,B,R), trpC, two predicted thiol protease genes, and 4 genes assigned to the phospholipase-D superfamily.
It is evident that there is a high level of functional conservation between C. pneumoniae and C. trachomatis as orthologs to C. trachomatis genes were identified for 859 (80%) of the predicted coding sequences for C. pneumoniae. The level of similarity for individual encoded proteins spans a wide spectrum (22-95% amino acid identity) with an average of 62% amino acid identity between orthologs from the two species. The percent amino acid identity between orthologous chlamydial proteins is similar among functional groups with the highest for proteins associated with translation and the lowest for proteins whose function in chlamydiae is uncharacterized and not related to proteins encoded by other organisms. The gene order of the homologous set of genes in C. pneumoniae shows reorganization relative to the genome of C. trachomatis; however, there is a high level of synteny for the gene organization of the two genomes. We identified thirty-nine blocks of 2 or more genes whose gene organization is colinear with homologs to C. trachomatis, although some of these are inverted. The distribution of genome reorganization is not evenly distributed on the chromosome as the region between C. pneumoniae coding sequences 0130-0300 contains substantially more reorganization than other areas of the genome. This region coincides with the predicted chromosome replication terminus.
We identified orthologs of enzymes characterized in other bacteria that account for the essential requirements for DNA replication, repair, transcription and translation including two predicted DNA helicases of the Swi2/Snf2 family found in C. trachomatis. Similar to C. trachomatis, alternative sigma subunits for RNA polymerase, σ28 and σ54, were identified in addition to anti-σ regulatory system factors RsbV, a RsbW-like single-domain histidine kinase, and a RsbU-like protein phosphatase. These findings suggest that the fundamental mechanisms of transcriptional regulation are conserved among Chlamydia. The C. trachomatis proteins containing SET and SWIB domains, and a SWIB domain fused to the C-terminus of the chlamydial topoisomerase I, not identified outside eukaryotes, are found in C. pneumoniae supporting their possible role in the chromatin condensation-decondensation characteristic of the biologically unique chlamydial developmental cycle.
The central metabolic pathways inferred from the C. pneumoniae genome sequence are the same as those identified for C. trachomatis C. pneumoniae has a glycolytic pathway and a linked tricarboxylic acid cycle, although likely functional, is incomplete as genes for citrate synthase, aconitase, and isocitrate dehydrogenase were not identified. C. pneumoniae has a complete glycogen synthesis and degradation system supporting a role for glycogen synthesis and utilization of glucose-derivatives in chlamydial metabolism. Genes encoding essential functions in aerobic respiration are present and electron flux may be supported by pyruvate, succinate, glycerol-3-phosphate, and NADH dehydrogenases, NADH-ubiquinone oxidoreductase and cytochrome oxidase. C. pneumoniae also contains the V (vacuolar)-type ATPase operon and the two ATP translocases found in C. trachomatis.
The type-III secretion virulence system required for invasion by several pathogenic bacteria and found in the C. trachomatis genome in three chromosomal locationsis also present in the C. pneumoniae genome. Each of the components is conserved and their relative genomic contexts are conserved. Genes such as a predicted serine/threonine protein kinase and other genes physically linked to genes encoding structural components of the type-III secretion apparatus, but without identified homologs, are also highly similar between the two species suggesting the functional roles in modifying cellular biology are fundamentally conserved.
Chlamydia-encoded proteins that are not found in chlamydial organisms but localized to the intracellular chlamydial inclusion membrane are likely essential for the unique intracellular biology and perhaps differences in inclusion morphology observed between species of Chlamydia. Several such proteins, termed IncA,B&C, have been characterized for a C. psittaci strain (Rockey, et al. Mol. Microbiol. 15:617-626 (1995); Rockey et al. Infect. Immun. 62:106-112 (1994)). C. pneumoniae and C. trachomatis encode orthologs to C. psittaci IncB and IncC and C. trachomatis also contains an ortholog to IncA. C. pneumoniae contains two genes that encode proteins with similarity to IncA (CPn0186 and CPn0585), although the level of homology is low suggesting analogous but possibily altered functions.
The tryptophan biosynthesis operon (trpA, trpB, trpR) and trpC identified in C. trachomatis is conspicuously missing in the C. pneumoniae genome. This represents the entire repertoire of genes associated with tryptophan biosynthesis identified in C. trachomatis. Seventeen genes adjacent to the C. trachomatis tryptophan operon also were not found in the C. pneumoniae genome. This region is the single largest loss of a contiguous genomic segment and includes 4 HKD superfamily encoding genes that encompass a family of proteins related to endonuclease and phospholipase D. These findings may be important for the ability of Chlamydia to persist in their hosts and cause disease by eliciting potent, focal and persistent inflammatory responses thought to be essential for pathogenesis.
The C. pneumoniae genome contains 187,711 additional nucleotides compared to the C. trachomatis genome, and the 214 coding sequences not found in C. trachomatis account for most of the increased genome size. Eighty-eight of these genes are found in blocks of >10 genes (11-30 genes/block), 41 are single genes, and the remainder are partnered with at least one other gene. Based upon the observation that ∼70% of all the C. pneumoniae genes have an identifiable homolog in GenBank, exclusive of C. trachomatis, it would be expected that over 150 of the 214 genes should have a homolog in GenBank, many associated with a function. However, only 28 coding sequences have similarity to genes from other organisms. Thus the majority of the genes that are mutually exclusive of C. trachomatis (186 of 214), and the 60 of 70 C. trachomatis genes that lacked an identifiable homolog in C. pneumoniae, do not have detectable homologs to genes from other organisms. We predict that most of the unique genes are essential for specific attributes that define the differential biology, tropism and pathogenesis of C. trachomatis and C. pneumoniae. Moreover, this suggests that C. pneumoniae has more unique biological (i.e., virulence) capacity than C. trachomatis. The ability of C. pneumoniae to be more invasive and survive in a broader range of host cell types than C. trachomatis is consistent with this hypothesis. Not all of the differences in biological capacity may be associated with mutually exclusive genes. One explanation for the significantly lower level of homology between protein sequences assigned as having C. pneumoniae and C. trachomatis orthologs but no identifiable orthologs in other organisms is that this set of proteins is not only associated with biological requirements specific for Chlamydia but this polymorphism may account for differential biology between the two species. The determination of the genome sequence from a representative of the C psittaci group will precisely delineate those genes that are mutually exclusive and specific for each species.
The major functionally identifiable addition to the C. pneumoniae genome is a large expansion of genes encoding a new family of chlamydial polymorphic membrane proteins (Pmp), alone representing 22% of the increased coding capacity. While the C. trachomatis genome has 9 pmp genes, remarkably the C. pneumoniae genome contains 21 pmp genes. Most of these genes appear to be amplified in two regions of the genome with three stand-alone genes. Interestingly one of the stand-alone genes is most closely related to the C. trachomatis pmpD which is the only stand-alone pmp gene in the C. trachomatis genome and it is located with the same relative genomic context, suggesting an essential and conserved function for this paralog. Six Pmp-coding genes are presumably not functional as five contain predicted coding frame-shifts and one is truncated. The amplification of this gene family and the confidently predicted frame-shifts suggest a specific molecular mechanism to promote functional or antigenic diversity. The biological role of this protein family remains enigmatic, although at least one of the proteins in C. psittaci related to this family is exposed on the chlamydial surface.
While a function could not be assigned for most of the unique C. pneumoniae genes, several have significant similarity to genes from other organisms. Functional assignments could be made for genes encoding GMP synthetase, IMP dehydrogenase, UMP synthase, uridine kinase, biotin synthase pathway proteins, methylthioadenosine nucleosidase, a DNA glycosylase and aromatic amino acid hydroxylase. Thus a complete pathway was identified for biotin biosynthesis. The additional purine and pyrimidine salvage pathway genes presumably reflect metabolic limitations in one of the cell types that C. pneumoniae infects or differences in the ability of C. pneumoniae to transport precursor nucleosides or nucleotides.
The addition of aromatic amino acid hydroxylase in C. pneumoniae is intriguing especially in light of the loss of tryptophan biosynthetic genes and the inability to synthesize other amino acids including phenylalanine. Aromatic amino acid hyroxlyases include three distinct enzymes that function to receptively oxidize phenylalanine to tyrosine, tyrosine to Dopa, and tryptophan to 5-hydroxytryptophan and serotonin. Although the chlamydial protein is similar to proteins of this family and incrementally more closely related to tryptophan hydroxylase, its specific function could not be confidently predicted. We hypothesize that it may be involved in C. pneumoniae virulence. Tryptophan hydroxylase has not been previously identified in bacteria and the origin of the chlamydial gene appears to be from eukaryotes. The functional role of an aromatic amino acid hydroxylase for C. pneumoniae is linked to the unique intracellular biology of this organism and may represent a key contribution to C. pneumoniae persistence and pathogenesis.
It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.
Table 1 provides functional assignments of C. pneumoniae nonprotein-encoding genomic sequences. Table 2 provides functional assignments of protein coding sequences. The Sequence Listing provides the amino acid sequences of the proteins corresponding to the coding sequences (SEQ ID NOS:2-1074).
| TABLE 1 | |||
| SEQ ID NO:1 | SEQ ID NO:1 | ||
| type | start position | end position | Gene |
| Ori | 841664 | 841396 | (R) Putative Origin of Replica |
| tmRNA | 138493 | 138074 | (R) tmRNA |
| pRNA | 607342 | 607649 | Ribonuclease P RNA |
| rRNA | 1000564 | 1002115 | 16S rRNA |
| rRNA | 1002415 | 1005278 | 23S rRNA |
| rRNA | 1005393 | 1005509 | 5S rRNA |
| tRNA | 269070 | 269142 | Ala tRNA_1 |
| tRNA | 164318 | 164389 | Asn tRNA |
| tRNA | 296224 | 296151 | (R) Asp tRNA |
| tRNA | 836191 | 836119 | (R) Ala tRNA_2 |
| tRNA | 1030533 | 1030603 | Cys tRNA |
| tRNA | 784896 | 784822 | (R) Glu tRNA |
| tRNA | 781680 | 781610 | (R) Gly tRNA_1 |
| tRNA | 961536 | 961607 | Gly tRNA_2 |
| tRNA | 999949 | 1000023 | His tRNA |
| tRNA | 268992 | 269065 | Ile tRNA |
| tRNA | 672236 | 672318 | Leu tRNA_1 |
| tRNA | 680178 | 680257 | Leu tRNA_2 |
| tRNA | 715889 | 715971 | Leu tRNA_3 |
| tRNA | 739403 | 739486 | Leu tRNA_4 |
| tRNA | 1175863 | 1175944 | Leu tRNA_5 |
| tRNA | 784994 | 784922 | (R) Lys tRNA |
| tRNA | 843926 | 843999 | Pro tRNA_2 |
| tRNA | 409922 | 409848 | (R) Pro tRNA_1 |
| tRNA | 631373 | 631445 | Phe tRNA |
| tRNA | 677337 | 677264 | (R) Arg tRNA_2 |
| tRNA | 807413 | 807341 | (R) Arg tRNA_3 |
| tRNA | 877473 | 877400 | (R) Arg tRNA_4 |
| tRNA | 462141 | 462214 | Arg tRNA_1 |
| tRNA | 1085605 | 1085676 | Gln tRNA |
| tRNA | 786780 | 786708 | (R) Thr tRNA_3 |
| tRNA | 89728 | 89657 | (R) Thr tRNA_1 |
| tRNA | 293477 | 293405 | (R) Thr tRNA_2 |
| tRNA | 87522 | 87450 | (R) Met tRNA_1 |
| tRNA | 199301 | 199229 | (R) Met tRNA_2 |
| tRNA | 199390 | 199317 | (R) Met tRNA_3 |
| tRNA | 626904 | 626987 | Ser tRNA_1 |
| tRNA | 708359 | 708440 | Ser tRNA_2 |
| tRNA | 1142034 | 1142117 | Ser tRNA_3 |
| tRNA | 1230028 | 1229945 | (R) Ser tRNA_4 |
| tRNA | 91070 | 90999 | (R) Trp tRNA |
| tRNA | 293399 | 293317 | (R) Tyr tRNA |
| tRNA | 296147 | 296075 | (R) Val tRNA_1 |
| tRNA | 1137389 | 1137462 | Val tRNA_2 |
| TABLE 2 | ||||
| Gene # | From | To | Strand | Gene Function (C. Trachomatis Ortholog in parenthesis) |
| CPn0001 | 282 | 4 | R | CT001 hypothetical protein |
| CPn0002 | 573 | 875 | F | gatC-Glu-tRNA Gln Amidotransferase (C subunit)-(CT002) |
| CPn0003 | 895 | 2370 | F | gatA-Glu tRNA Gln Amidotransferase-(CT003) |
| CPn0004 | 2370 | 3833 | F | gatB-(Pet 112) Glu tRNA Gln Amidotransferase (B Subunit) |
| CPn0005 | 4127 | 6892 | F | pmp_1-Polymorphic Outer Membrane Protein G Family |
| CPn0006 | 7293 | 7141 | R | |
| CPn0007 | 7605 | 10496 | F | |
| CPn0008 | 10975 | 11685 | F | |
| CPn0009 | 11815 | 13119 | F | |
| CPn0010 | 13435 | 14325 | F | |
| CPn0010 | 14379 | 15746 | F | frame-shift with 0010 |
| CPn0011 | 15892 | 16614 | F | |
| CPn0012 | 16644 | 18212 | F | |
| CPn0013 | 18584 | 21106 | F | pmp_2-Polymorphic Outer Membrane Protein G Family |
| CPn0014 | 21392 | 21922 | F | pmp_3-Polymorphic Outer Membrane Protein G Family |
| CPn0015 | 21835 | 24174 | F | pmp_3-PMP_3 (frame-shift with 0014) |
| CPn0016 | 24416 | 26188 | F | pmp_4-Polymorphic Outer Membrane Protein G Family |
| CPn0017 | 26094 | 27170 | F | pmp_4-PMP_4 (frame-shift with 0016) |
| CPn0018 | 27522 | 29003 | F | pmp_5-Polymorphic Outer Membrane Protein G Family |
| CPn0019 | 29007 | 30356 | F | pmp_5-PMP_5 (frame-shift with 0018) |
| CPn0020 | 32687 | 30603 | R | Predicted OMP [leader (14) peptide: outer membrane]-(CT351) |
| CPn0021 | 34410 | 32707 | R | Predicted OMP [leader (19) peptide]-(CT350) |
| CPn0022 | 34982 | 34395 | R | maf-(CT349) |
| CPn0023 | 36603 | 35014 | R | yjjK/alr-ABC Transporter Protein ATPase-(CT348) |
| CPn0024 | 37596 | 36661 | R | xerC-Integrase/recombinase-(CT347) |
| CPn0025 | 38604 | 37684 | R | elaC/atsA-Sulphohydrolase/Glycosulfatase-(CT346) |
| CPn0026 | 39625 | 38762 | R | CT345 hypothetical protein-(CT345) |
| CPn0027 | 42234 | 39778 | R | lon-Lon ATP-dependent Protease-(CT344) |
| CPn0028 | 43325 | 42543 | R | |
| CPn0029 | 43755 | 43390 | R | |
| CPn0030 | 43891 | 44529 | F | gcp_1-O-Sialoglycoprotein Endopeptidase_1-(CT343) |
| CPn0031 | 44711 | 44884 | F | rs21-S21 Ribosomal Protein-(CT342) |
| CPn0032 | 44923 | 46098 | F | dnaJ-Heat Shock Protein J-(CT341) |
| CPn0033 | 46138 | 48171 | F | pdhA&B/odbA&odbB-(pyruvate) Oxoisovalerate |
| Dehydrogenase Alpha & Fusion-(CT340) | ||||
| CPn0034 | 49457 | 48210 | R | |
| CPn0035 | 51029 | 49569 | R | CT339 hypothetical protein |
| CPn0036 | 51002 | 51796 | F | CT338 hypothetical protein |
| CPn0037 | 51792 | 52115 | F | ptsH-PTS Phosphocarrier Protein Hpr-(CT337) |
| CPn0038 | 52119 | 53831 | F | ptsI-PTS PEP Phosphotransferase-(CT336) |
| CPn0039 | 54250 | 53963 | R | ybaB-(CT335) |
| CPn0040 | 55643 | 54318 | R | dnaX_1-DNA Pol III Gamma and Tau_1-(CT334) |
| CPn0041 | 55996 | 57342 | F | |
| CPn0042 | 57403 | 58182 | F | |
| CPn0043 | 58447 | 60372 | F | |
| CPn0044 | 60419 | 60778 | F | |
| CPn0045 | 61069 | 62790 | F | |
| CPn0046 | 62790 | 63263 | F | |
| CPn0047 | 63455 | 63652 | F | |
| CPn0048 | 63687 | 65801 | F | *yqfF-Bs conserved hypothetical IM protein |
| CPn0049 | 66296 | 65817 | R | |
| CPn0050 | 66813 | 66499 | R | |
| CPn0051 | 66833 | 67111 | F | |
| CPn0052 | 68005 | 67304 | R | hemC-Porphobilinogen Deaminase-(CT299) |
| CPn0053 | 69344 | 67986 | R | sms-Sms Protein-(CT298) |
| CPn0054 | 70023 | 69313 | R | rnc-Ribonuclease III-(CT297) |
| CPn0055 | 70129 | 70590 | F | CT296 hypothetical protein |
| CPn0056 | 70953 | 72746 | F | mrsA-Phosphomannomutase-(CT295) |
| CPn0057 | 72934 | 73554 | F | sodM-Superoxide Dismutase (Mn)-(CT294) |
| CPn0058 | 73639 | 74562 | F | accD-AcCoA Carboxylase/Transferase Beta-(CT293) |
| CPn0059 | 74616 | 75050 | F | dut-duTP Nucleotidohydrolase-(CT292) |
| CPn0060 | 75055 | 75528 | F | ptsN_1-PTS IIA Protein-(CT291) |
| CPn0061 | 75534 | 76208 | F | ptsN_2-PTS IIA Protein + HTH DNA-Binding Domain-(CT290) |
| CPn0062 | 76308 | 77690 | F | CT289 hypothetical protein |
| CPn0063 | 78112 | 78267 | F | |
| CPn0064 | 78346 | 78576 | F | |
| CPn0065 | 78924 | 80651 | F | CT288 hypothetical protein |
| CPn0066 | 80925 | 82655 | F | |
| CPn0067 | 82953 | 84053 | F | |
| CPn0068 | 84903 | 84331 | R | CT360 hypothetical protein |
| CPn0069 | 85236 | 87086 | F | |
| CPn0070 | 87378 | 87208 | R | |
| CPn0071 | 88045 | 87599 | R | CT325 hypothetical protein |
| CPn0072 | 89061 | 88057 | R | CT324 hypothetical protein |
| CPn0073 | 89356 | 89574 | F | infA-Initiation Factor IF-1-(CT323) |
| CPn0074 | 89774 | 90955 | F | tufA-Elongation Factor Tu-(CT322) |
| CPn0075 | 91102 | 91350 | F | secE-preprotein translocase-(CT321) |
| CPn0076 | 91358 | 91903 | F | nusG-Transcriptional Antitermination-(CT320) |
| CPn0077 | 92013 | 92435 | F | rl11-L11 Ribosomal Protein-(CT319) |
| CPn0078 | 92465 | 93160 | F | rl1-L1 Ribosomal Protein-(CT318) |
| CPn0079 | 93179 | 93688 | F | rl10-L10 Ribosomal Protein-(CT317) |
| CPn0080 | 93735 | 94121 | F | rl7-L7/L12 Ribosomal Protein-(CT316) |
| CPn0081 | 94261 | 98016 | F | rpoB-RNA Polymerase Beta-(CT315) |
| CPn0082 | 98043 | 102221 | F | rpoC-RNA Polymerase Beta'-(CT314) |
| CPn0083 | 102332 | 103312 | F | tal-Transaldolase-(CT313) |
| CPn0084 | 103362 | 103751 | F | predicted ferredoxin-(CT312) |
| CPn0085 | 104506 | 103766 | R | CT311 hypothetical protein |
| CPn0086 | 104904 | 105527 | F | atpE-ATP Synthase Subunit E-(CT310) |
| CPn0087 | 105579 | 106376 | F | CT309 hypothetical protein |
| CPn0088 | 106373 | 108145 | F | atpA-ATP Synthase Subunit A-(CT308) |
| CPn0089 | 108153 | 109466 | F | atpB-ATP Synthase Subunit B-(CT307) |
| CPn0090 | 109454 | 110080 | F | atpD-ATP Synthase Subunit D-(CT306) |
| CPn0091 | 110074 | 112053 | F | atpI-ATP Synthase Subunit I-(CT305) |
| CPn0092 | 112151 | 112573 | F | atpK-ATP Synthase Subunit K-(CT304) |
| CPn0093 | 112509 | 113015 | F | CT303 hypothetical protein |
| CPn0094 | 113152 | 115971 | F | valS-Valyl tRNA Synthetase-(CT302) |
| CPn0095 | 116037 | 118790 | F | pknO-S/T Protein Kinase-(CT301) |
| CPn0096 | 124314 | 118837 | R | uvrA-Excinuclease ABC Subunit A-(CT333) |
| CPn0097 | 124555 | 126006 | F | pyk-Pyruvate Kinase-(CT332) |
| CPn0098 | 127491 | 126091 | R | htrB-Acyltransferase-(CT010) |
| CPn0099 | 127593 | 127865 | F | |
| CPn0100 | 129141 | 127882 | R | CT011 hypothetical protein |
| CPn0101 | 129932 | 129141 | R | ybbP family hypothetical protein-(CT012) |
| CPn0102 | 130123 | 131466 | F | cydA-Cytochrome Oxidase Subunit I-(CT013) |
| CPn0103 | 131480 | 132511 | F | cydB-Cytochrome Oxidase Subunit II-(CT014) |
| CPn0104 | 133875 | 132676 | R | CT017 hypothetical protein |
| CPn0105 | 134847 | 134029 | R | CT016 hypothetical protein |
| CPn0106 | 135091 | 136374 | F | phoH-ATPase-(CT015) |
| CPn0107 | 137162 | 136392 | R | CT058 hypothetical protein_1 |
| CPn0108 | 137857 | 137303 | R | CT018 |
| CPn0109 | 138655 | 141783 | F | ileS-Isoleucyl-tRNA Synthetase-(CT019) |
| CPn0110 | 143734 | 141827 | R | lepB-Signal Peptidase I-(CT020) |
| CPn0111 | 144686 | 143934 | R | CT021 hypothetical protein |
| CPn0112 | 144767 | 145093 | F | rl31-L31 Ribosomal Protein-(CT022) |
| CPn0113 | 145335 | 146405 | F | pfrA-Peptide Chain Releasing Factor (RF-1)-(CT023) |
| CPn0114 | 146398 | 147261 | F | hemK-A/G specific methylase-(CT024) |
| CPn0115 | 147279 | 148622 | F | ffh-Signal Recognition Particle GTPase-(CT025) |
| CPn0116 | 148616 | 148972 | F | rs16-S16 Ribosomal Protein-(CT026) |
| CPn0117 | 148989 | 150071 | F | trmD-tRNA (guanine N-1)-Methyltransferase-(CT027) |
| CPn0118 | 150102 | 150464 | F | r119-L19 Ribosomal Protein-(CT028) |
| CPn0119 | 150523 | 151164 | F | rnhB_1-Ribonuclease HII_1-(CT029) |
| CPn0120 | 151164 | 151778 | F | gmk-GMP Kinase-(CT030) |
| CPn0121 | 151778 | 152068 | F | CT031 hypothetical protein |
| CPn0122 | 152071 | 153723 | F | metG-Methionyl-tRNA Synthetase-(CT032) |
| CPn0123 | 155969 | 153774 | R | recD_1-Exodeoxyribonuclease V (Alpha Subunit)_1-(CT033) |
| CPn0124 | 156614 | 158068 | F | |
| CPn0125 | 158096 | 158605 | F | |
| CPn0126 | 158809 | 161085 | F | |
| CPn0127 | 162143 | 161130 | R | ytfF-Cationic Amino Acid Transporter-(CT034) |
| CPn0128 | 162277 | 163053 | F | bpl1-Biotin Protein Ligase-(CT035) |
| CPn0129 | 163717 | 163064 | R | similarity to CT036 |
| CPn0130 | 164245 | 163751 | R | |
| CPn0131 | 164549 | 165580 | F | |
| CPn0132 | 165587 | 166561 | F | |
| CPn0133 | 167334 | 166564 | R | CHLPS hypothetical protein-(CT109) |
| CPn0134 | 169098 | 167467 | R | groEL_1-HSP-60_1-(CT110) |
| CPn0135 | 169448 | 169143 | R | groES-10 KDa Chaperonin-(CT111) |
| CPn0136 | 171401 | 169569 | R | pepF-Oligopeptidase-(CT112) |
| CPn0137 | 172254 | 171502 | R | ybgI-ACR family-(CT108) |
| CPn0138 | 174019 | 172700 | R | hemL-Glutamate-1-semialdehyde-2.1-aminomutase-(CT210) |
| CPn0139 | 174656 | 174093 | R | yqgE-(CT210) |
| CPn0140 | 175110 | 174673 | R | yqdE-(CT212) |
| CPn0141 | 175802 | 175110 | R | rpiA-Ribose-5-P Isomerase A-(CT213) |
| CPn0142 | 176091 | 175816 | R | |
| CPn0143 | 177335 | 176214 | R | *yxjG_Bs_1 Hypothetical Protein |
| CPn0144 | 177963 | 180560 | F | clpB-Clp Protease ATPase-(CT113) |
| CPn0145 | 180777 | 182369 | F | CT114 hypothetical protein |
| CPn0146 | 182613 | 183095 | F | |
| CPn0147 | 183225 | 183671 | F | |
| CPn0148 | 183846 | 185702 | F | pkn1-S/T Protein Kinase-(CT145) |
| CPn0149 | 185715 | 187700 | F | dnlJ-DNA Ligase-(CT146) |
| CPn0150 | 187834 | 192444 | F | CT147 hypothetical protein |
| CPn0151 | 194142 | 192625 | R | mhpA-Monooxygenase-(CT148) |
| CPn0152 | 195265 | 194318 | R | CT149 hypothetical protein |
| CPn0153 | 195433 | 197892 | F | leuS-Leucyl tRNA Synthetase-(CT209) |
| CPn0154 | 197892 | 199202 | F | gseA-KDO Transferase-(CT208) |
| CPn0155 | 199691 | 199488 | R | |
| CPn0156 | 200117 | 199770 | R | |
| CPn0157 | 200723 | 200298 | R | |
| CPn0158 | 201430 | 200894 | R | |
| CPn0159 | 201772 | 201467 | R | |
| CPn0160 | 203791 | 202127 | R | pfkA_1-Fructose-6-P Phosphotransferase_1-(CT207) |
| CPn0161 | 204622 | 203798 | R | predicted acyltransferase family-(CT206) |
| CPn0162 | 205828 | 204803 | R | |
| CPn0163 | 206026 | 206394 | F | |
| CPn0164 | 206498 | 206998 | F | |
| CPn0165 | 206998 | 207582 | F | |
| CPn0166 | 207630 | 207962 | F | |
| CPn0167 | 208306 | 207977 | R | |
| CPn0168 | 208641 | 208417 | R | |
| CPn0169 | 209501 | 208710 | R | |
| CPn0170 | 211026 | 210025 | R | |
| CPn0171 | 212435 | 211149 | R | *guaA-GMP Synthase |
| CPn0172 | 213177 | 212440 | R | *guaB/impD-Inosine 5'-monophosphase dehydrogenase (COOH-terminal region only) |
| CPn0173 | 213987 | 213715 | R | |
| CPn0174 | 214257 | 214724 | F | |
| CPn0175 | 214898 | 215275 | F | |
| CPn0176 | 215286 | 216518 | F | CT153 hypothetical protein |
| CPn0177 | 217459 | 216608 | R | |
| CPn0178 | 218052 | 217789 | R | |
| CPn0179 | 218403 | 218056 | R | |
| CPn0180 | 218851 | 218355 | R | |
| CPn0181 | 219175 | 218777 | R | |
| CPn0182 | 220695 | 219334 | R | accC-Biotin Carboxylase-(CT124) |
| CPn0183 | 221195 | 220695 | R | accB-Biotin Carboxyl Carrier Protein-(CT123) |
| CPn0184 | 221775 | 221221 | R | efp_1-Elongation Factor P_1-(CT122) |
| CPn0185 | 222451 | 221765 | R | rpe/araD-Ribulose-P Epimerase-(CT121) |
| CPn0186 | 222899 | 224068 | F | *similarity to Cps IncA_1-(CT119) |
| CPn0187 | 224248 | 225045 | F | predicted methylase-(CT133) |
| CPn0188 | 225111 | 226400 | F | CT132 hypothetical protein |
| CPn0189 | 226400 | 229825 | F | CT131 homolog-(Possible Transmembrane Protein) |
| CPn0190 | 229919 | 231274 | F | |
| CPn0191 | 231991 | 231314 | R | glnQ-ABC Amino Acid Transporter ATPase-(CT130) |
| CPn0192 | 232634 | 231984 | R | glnP-ABC Amino Acid Transporter Permease-(CT129) |
| CPn0193 | 233126 | 232686 | R | *argR-Arginine Repressor |
| CPn0194 | 233210 | 234241 | F | gcp_2-O-Sialoglycoprotein Endopeptidase_2-(CT197) |
| CPn0195 | 234190 | 235785 | F | oppA_1-Oligopeptide Binding Protein_1 |
| CPn0196 | 235939 | 237519 | F | oppA_2-Oligopeptide Binding Protein_2-(CT198) |
| CPn0197 | 237578 | 238882 | F | oppA_3-Oligopeptide Binding Protein_3 |
| CPn0198 | 239169 | 240746 | F | oppA_4-Oligopeptide Binding Protein_4 |
| CPn0199 | 241042 | 241983 | F | oppB_1-Oligopeptide Permease_1-(CT199) |
| CPn0200 | 242017 | 242868 | F | oppC_1-Oligopeptide Permease_1-(CT200) |
| CPn0201 | 242864 | 243715 | F | oppD-Oligopeptide Transport ATPase-(CT201) |
| CPn0202 | 243715 | 244500 | F | oppF-Oligopeptide Transport ATPase-(CT202) |
| CPn0203 | 245008 | 245802 | F | |
| CPn0204 | 245817 | 246002 | F | |
| CPn0205 | 246133 | 246327 | F | |
| CPn0206 | 246409 | 247161 | F | CT203 hypothetical protein |
| CPn0207 | 247208 | 248617 | F | ybhI/sodiT1-Oxoglutarate/Malate Translocator-(CT204) |
| CPn0208 | 248953 | 250602 | F | pfkA_2-Fructose-6-P Phosphotransferase_2-(CT205) |
| CPn0209 | 251036 | 251272 | F | |
| CPn0210 | 252384 | 251440 | R | |
| CPn0211 | 252756 | 252463 | R | |
| CPn0212 | 254066 | 252888 | R | |
| CPn0213 | 254342 | 254190 | R | |
| CPn0214 | 255657 | 254446 | R | |
| CPn0215 | 257015 | 255759 | R | |
| CPn0216 | 257608 | 257174 | R | |
| CPn0217 | 257896 | 258579 | F | ypdP-(CT140) |
| CPn0218 | 259058 | 258582 | R | |
| CPn0219 | 259357 | 260472 | F | tgt-Queuine tRNA Ribosyl Transferase-(CT193) |
| CPn0220 | 260696 | 261238 | F | |
| CPn0221 | 261657 | 262064 | F | |
| CPn0222 | 262504 | 262842 | F | *weak similarity to Bacteriophage CHP1 (Orf4) |
| CPn0223 | 262956 | 263333 | F | |
| CPn0224 | 263435 | 263674 | F | |
| CPn0225 | 263873 | 264541 | F | |
| CPn0226 | 264566 | 264967 | F | |
| CPn0227 | 265416 | 265009 | R | dsbB-Disulfide bond Oxidoreductase-(CT176) |
| CPn0228 | 266110 | 265412 | R | dsbG-Disulfide Bond Chaperone-(CT177) |
| CPn0229 | 266328 | 267560 | F | CT178 hypothetical protein |
| CPn0230 | 268253 | 267576 | R | CT179 hypothetical protein |
| CPn0231 | 268957 | 268253 | R | tauB-ABC Transport ATPase (Nitrate/Fe)-(CT180) |
| CPn0232 | 270122 | 269232 | R | *similarity to 5'-Methylthioadenosine/S-Adenosylhomocysteine |
| Nucleosidase | ||||
| CPn0233 | 270424 | 270248 | R | |
| CPn0234 | 271240 | 270548 | R | CT181 hypothetical protein |
| CPn0235 | 271416 | 272177 | F | kdsB-deoxyoctulonosic Acid Synthetase-(CT182) |
| CPn0236 | 272156 | 273766 | F | pyrG-CTP Synthetase-(CT183) |
| CPn0237 | 273762 | 274214 | F | yggF Family-(CT184) |
| CPn0238 | 274303 | 275838 | F | rwf-Glucose-6-P Dehydrogenase-(CT185) |
| CPn0239 | 275899 | 276672 | F | devB-Glucose-6-P Dehydrogenase (DevB family)-(CT186) |
| CPn0240 | 277861 | 276698 | R | |
| CPn0241 | 279354 | 278203 | R | |
| CPn0242 | 279918 | 279487 | R | |
| CPn0243 | 280555 | 280133 | R | |
| CPn0244 | 280918 | 281556 | F | adk-Adenylate Kinase-(CT128) |
| CPn0245 | 281645 | 282499 | F | ydhO-Polysaccharide Hydrolase-Invasin Repeat Family-(CT127) |
| CPn0246 | 282952 | 282551 | R | rs9-S9 Ribosomal Protein-(CT126) |
| CPn0247 | 283415 | 282969 | R | rl13-L13 Ribosomal Protein-(CT125) |
| CPn0248 | 284327 | 283650 | R | ycfV/ybbA-ABC Transporter ATPase-(CT152) |
| CPn0249 | 285841 | 284333 | R | CT151 hypothetical protein |
| CPn0250 | 286057 | 285902 | R | rl33-L33 Ribosomal Protein-(CT150) |
| CPn0251 | 286060 | 287559 | F | *conserved hypothetical protein |
| CPn0252 | 288112 | 287576 | R | CT144 hypothetical protein (frame-shift with 0253?) |
| CPn0253 | 288456 | 287950 | R | CT144 hypothetical protein_1 |
| CPn0254 | 289262 | 288459 | R | CT143 hypothetical protein_1 |
| CPn0255 | 290165 | 289329 | R | CT142 hypothetical protein_1 |
| CPn0256 | 291264 | 290398 | R | CT144 hypothetical protein_2 |
| CPn0257 | 292127 | 291267 | R | CT143 hypothetical protein_2 |
| CPn0258 | 292534 | 292133 | R | CT142 hypothetical protein (frame-shift with 0259?) |
| CPn0259 | 292986 | 292441 | R | CT142 hypothetical protein_2 |
| CPn0260 | 294045 | 293548 | R | secA_1-Protein Translocase Subunit_1-(CT141) |
| CPn0261 | 294302 | 295033 | F | ydaO-PP-Loop Superfamily ATPase-(CT217) |
| CPn0262 | 295091 | 295933 | F | surE-SurE-like Acid Phosphatase-(CT218) |
| CPn0263 | 296249 | 297136 | F | yqfU hypothetical protein-(CT221) |
| CPn0264 | 297730 | 297155 | R | ubiD-Phenylacrylate Decarboxylase-(CT220) |
| CPn0265 | 298620 | 297730 | R | ubiA-Benzoate Octaphenyltransferase-(CT219) |
| CPn0266 | 299184 | 299876 | F | |
| CPn0267 | 300122 | 300910 | F | |
| CPn0268 | 300935 | 301318 | F | |
| CPn0269 | 302450 | 301476 | R | Dipeptidase-(CT138) |
| CPn0270 | 303325 | 302468 | R | ywlC-SuA5 Superfamily-related Protein-(CT137) |
| CPn0271 | 303634 | 304362 | F | Lysophospholipase esterase-(CT136) |
| CPn0272 | 305233 | 304340 | R | dnaX_2-DNA Pol III Gamma and Tau_2-(CT187) |
| CPn0273 | 305844 | 305227 | R | tdk-Thymidylate Kinase-(CT188) |
| CPn0274 | 308353 | 305852 | R | gyrA_1-DNA Gyrase Subunit A_1-(CT189) |
| CPn0275 | 310786 | 308372 | R | gyrB_1-DNA Gyrase Subunit B_1-(CT190) |
| CPn0276 | 311137 | 310793 | R | CT191 hypothetical protein |
| CPn0277 | 311910 | 311404 | R | |
| CPn0278 | 312875 | 312060 | R | *conserved outer membrane lipoprotein protein |
| CPn0279 | 313537 | 312875 | R | *Possible ABC Transporter Permease Protein |
| CPn0280 | 314572 | 313550 | R | dppF-Dipeptide Transporter ATPase-(CT689) |
| CPn0281 | 315057 | 316103 | F | dhnA-Predicted 1,6-Fructose Biphosphaid Aldolase (dehydrin family)-(CT215) |
| CPn0282 | 316126 | 317529 | F | xasA/gadC-Amino Acid Transporter-(CT216) |
| CPn0283 | 318497 | 317532 | R | |
| CPn0284 | 319045 | 318551 | R | |
| CPn0285 | 320595 | 319051 | R | |
| CPn0286 | 322059 | 320650 | R | mgtE-Mg++ Transporter (CBS Domain)-(CT194) |
| CPn0287 | 324221 | 322089 | R | |
| CPn0288 | 325716 | 324571 | R | CT195 hypothetical protein |
| CPn0289 | 325812 | 326996 | F | aaaT-Neutral Amino Acid (Glutamate) Transporter-(CT230) |
| CPn0290 | 327042 | 328523 | F | Na-dependent Transporter-(CT231) |
| CPn0291 | 328667 | 329194 | F | incB-Inclusion Membrane Protein B-(CT232) |
| CPn0292 | 329228 | 329836 | F | incC-Inclusion Membrane Protein C-(CT233) |
| CPn0293 | 329949 | 332723 | F | CT234 hypothetical protein |
| CPn0294 | 333092 | 333502 | F | cAMP-Dependent Protein Kinase Regulatory Subunit-(CT235) |
| CPn0295 | 333863 | 333627 | R | acpP-Acyl Carrier Protein-(CT236) |
| CPn0296 | 334765 | 334022 | R | fabG-Oxoacyl (Carrier Protein) Reductase-(CT237) |
| CPn0297 | 335697 | 334774 | R | fabD-Malonyl Acyl Carrier Transcyclase-(CT238) |
| CPn0298 | 336721 | 335717 | R | fabH-Oxoacyl Carrier Protein Synthase III-(CT239) |
| CPn0299 | 336816 | 337415 | F | recR-Recombination Protein-(CT240) |
| CPn0300 | 337783 | 340152 | F | yaeT-Omp85 Analog-(CT241) |
| CPn0301 | 340250 | 340762 | F | (OmpH-Like Outer Membrane Protein)-(CT242) |
| CPn0302 | 340787 | 341866 | F | lpxD-UDP Glucosamine N-Acyltransferase-(CT243) |
| CPn0303 | 342958 | 341921 | R | CT244 hypothetical protein |
| CPn0304 | 343133 | 344158 | F | pdhA/odpA-Pyruvate Dehydrogenase Alpha-(CT245) |
| CPn0305 | 344154 | 345137 | F | pdhB/odpB-Pyruvate Dehydrogenase Beta-(CT246) |
| CPn0306 | 345145 | 346431 | F | pdhC-Dihydrolipoamide Acetyltransferase-(CT247) |
| CPn0307 | 348986 | 346515 | R | glgP-Glycogen Phosphorylase-(CT248) |
| CPn0308 | 349234 | 349596 | F | similarity to CT249 |
| CPn0309 | 350974 | 349595 | R | dnaA_1-Replication Initiation Protein_1-(CT250) |
| CPn0310 | 353433 | 351049 | R | 60IM-60 kDa Inner Membrane Protein-(CT251) |
| CPn0311 | 354438 | 353575 | R | lgt-Prolipoprotein Diacylglycerol Transferase-(CT252) |
| CPn0312 | 354524 | 354976 | F | CT101 hypothetical protein |
| CPn0313 | 354990 | 355355 | F | acpS-Acyl-carrier Protein Synthase-(CT100) |
| CPn0314 | 356285 | 355353 | R | trxB-Thioredoxin Reductase-(CT099) |
| CPn0315 | 356977 | 358716 | F | rs1-S1 Ribosomal Protein-(CT098) |
| CPn0316 | 358820 | 360121 | F | nusA-N Utilization Protein A-(CT097) |
| CPn0317 | 360081 | 362750 | F | infB-Initiation Factor-2-(CT096) |
| CPn0318 | 362767 | 363126 | F | rbfA-Ribosome Binding Factor A-(CT095) |
| CPn0319 | 363175 | 363879 | F | truB-tRNA Pseudouridine Synthase-(CT094) |
| CPn0320 | 363860 | 364783 | F | ribF-FAD Synthase-(CT093) |
| CPn0321 | 365858 | 364767 | R | ychF-GTP Binding Protein-(CT092) |
| CPn0322 | 366249 | 367328 | F | yscU-YopS Translocation Protein U-(CT091) |
| CPn0323 | 367331 | 369460 | F | lcrD-Low Calcium Response D-(CT090) |
| CPn0324 | 369492 | 370688 | F | lcrE-Low Calcium Response E-(CT089) |
| CPn0325 | 370708 | 371148 | F | sycE-Secretion Chaperone-(CT088) |
| CPn0326 | 371148 | 372725 | F | malQ-Glucanotransferase-(CT087) |
| CPn0327 | 372945 | 373211 | F | rl28-L28 Ribosomal Protein-(CT086) |
| CPn0328 | 373241 | 374992 | F | CT085 hypothetical protein |
| CPn0329 | 375088 | 376146 | F | Phopholipase D Superfamily [leader (33) peptide]-(CT084) |
| CPn0330 | 376675 | 376202 | R | CT083 hypothetical protein |
| CPn0331 | 378437 | 376701 | R | CT082 hypothetical protein |
| CPn0332 | 378655 | 378536 | R | CHLTR T2 Protein-(CT081) |
| CPn0333 | 379090 | 378800 | R | ltuB-(CT080) |
| CPn0334 | 379311 | 379823 | F | CT079 similarity |
| CPn0335 | 379817 | 380674 | F | folD-Methylene Tetrahydrofolate Dehydrogenase-(CT078) |
| CPn0336 | 380650 | 381591 | F | yojL-(CT077) |
| CPn0337 | 382027 | 381575 | R | smpB-Small Protein B-(CT076) |
| CPn0338 | 382278 | 383375 | F | dnaN-DNA Pol III (beta chain)-(CT075) |
| CPn0339 | 383420 | 384034 | F | recF-ABC superfamily ATPase-(CT074) |
| CPn0340 | 383842 | 384156 | F | (frame-shift with 0339) |
| CPn0341 | 384160 | 384495 | F | (frame-shift with 0340) |
| CPn0342 | 384622 | 385062 | F | predicted OMP [leader (19) peptide]-(CT073) |
| CPn0343 | 384999 | 385595 | F | (frame-shift with 0342?) |
| CPn0344 | 387420 | 385558 | R | yaeL-Metalloprotease-(CT072) |
| CPn0345 | 388572 | 387436 | R | yaeM-(CT071) |
| CPn0346 | 389675 | 388704 | R | troD/ytgD-Integral Membrane Protein-(CT070) |
| CPn0347 | 391021 | 389678 | R | troC/ytgC-Integral Membrane Protein-(CT069) |
| CPn0348 | 391803 | 391027 | R | troB/ytgB-ABC transporter ATPase-(CT068) |
| CPn0349 | 392770 | 391790 | R | troA/ytgA-Solute Protein Binding Family-(CT067) |
| CPn0350 | 393181 | 393684 | F | CT066 hypothetical protein |
| CPn0351 | 393888 | 395432 | F | adt_1-ADP-ATP Translocase_1-(CT065) |
| CPn0352 | 395574 | 396830 | F | |
| CPn0353 | 396893 | 397135 | F | |
| CPn0354 | 397167 | 398507 | F | |
| CPn0355 | 399889 | 398591 | R | |
| CPn0356 | 400459 | 400109 | R | |
| CPn0357 | 401317 | 400469 | R | |
| CPn0358 | 401751 | 401578 | R | |
| CPn0359 | 402012 | 403817 | F | lepA-GTPase-(CT064) |
| CPn0360 | 405358 | 403922 | R | gnd-6-Phosphogluconate Dehydrogenase-(CT063) |
| CPn0361 | 406647 | 405382 | R | tyrS-tyrosyl tRNA Synthetase-(CT062) |
| CPn0362 | 407825 | 407055 | R | fliA/rpsD-Sigma-28/WhiG Family-(CT061) |
| CPn0363 | 409688 | 407943 | R | flhA-Flagellar Secretion Protein-(CT060) |
| CPn0364 | 409966 | 410238 | F | fer4-Ferredoxin IV-(CT059) |
| CPn0365 | 410528 | 411544 | F | |
| CPn0366 | 411976 | 412440 | F | |
| CPn0367 | 413102 | 413836 | F | |
| CPn0368 | 413790 | 414107 | F | |
| CPn0369 | 414351 | 415562 | F | CT058 hypothetical protein_2 |
| CPn0370 | 415800 | 416912 | F | CT058 hypothetical protein_3 |
| CPn0371 | 417147 | 417503 | F | |
| CPn0372 | 417687 | 418001 | F | |
| CPn0373 | 418380 | 420218 | F | gcpE-(CT057) |
| CPn0374 | 420218 | 420961 | F | CT056 hypothetical protein |
| CPn0375 | 421121 | 421615 | F | |
| CPn0376 | 421854 | 422294 | F | |
| CPn0377 | 423438 | 422347 | R | sucB_1-Dihydrolipoamide Succinyltransferase_1-(CT055) |
| CPn0378 | 426168 | 423445 | R | sucA-Oxoglutarate Dehydrogenase-(CT054) |
| CPn0379 | 426322 | 426765 | F | CT053 hypothetical protein |
| CPn0380 | 426758 | 427876 | F | hemN_1-Coproporphyrinogen III Oxidase_1-(CT052) |
| CPn0381 | 429809 | 428037 | R | CT326 similarity |
| CPn0382 | 430749 | 430036 | R | yabC/yraL-SAM-Dependent Methytransferase-(CT048) |
| CPn0383 | 431693 | 430749 | R | CT047 hypothetical protein |
| CPn0384 | 432377 | 431862 | R | hctB-Histone-like Protein 2-(CT046) |
| CPn0385 | 434018 | 432522 | R | pepA-Leucyl Aminopeptidase A-(CT045) |
| CPn0386 | 434525 | 434046 | R | ssb-SS DNA Binding Protein-(CT044) |
| CPn0387 | 435196 | 434699 | R | CT043 hypothetical protein |
| CPn0388 | 435329 | 437320 | F | glgX-Glycogen Hydrolase (debranching)-(CT042) |
| CPn0389 | 438134 | 437319 | R | CT041 hypothetical protein |
| CPn0390 | 439144 | 438134 | R | ruvB-Holliday Junction Helicase-(CT040) |
| CPn0391 | 439692 | 439510 | R | |
| CPn0392 | 439814 | 440383 | F | dcd-dCTP Deaminase-(CT039) |
| CPn0393 | 440379 | 440723 | F | CT038 hypothetical protein |
| CPn0394 | 440736 | 441968 | F | tlyC_1-CBS Domain protein (Hemolysin Homolog)_1-(CT256) |
| CPn0395 | 441964 | 443175 | F | CT257 hypothetical protein |
| CPn0396 | 444353 | 443241 | R | yhfO-NifS-related protein-(CT258) |
| CPn0397 | 445115 | 444381 | R | PP2C phosphatase family-(CT259) |
| CPn0398 | 445533 | 445700 | F | |
| CPn0399 | 445879 | 446523 | F | CT253 hypothetical protein |
| CPn0400 | 446536 | 447306 | F | CT254 hypothetical protein |
| CPn0401 | 447884 | 447495 | R | CT255 hypothetical protein |
| CPn0402 | 448994 | 447888 | R | mutY-Adenine Glycosylase-(CT107) |
| CPn0403 | 449015 | 449710 | F | yceC-predicted pseudouridine synthetase family-(CT106) |
| CPn0404 | 450887 | 449871 | R | |
| CPn0405 | 451739 | 450966 | R | CT105 hypothetical protein |
| CPn0406 | 451969 | 452865 | F | fabI-Enoyl-Acyl-Carrier Protein Reductase-(CT104) |
| CPn0407 | 453742 | 452858 | R | HAD superfamily hydrolase/phosphatase-(CT103) |
| CPn0408 | 454105 | 454581 | F | CT102 hypothetical protein |
| CPn0409 | 454645 | 455127 | F | CT260 hypothetical protein |
| CPn0410 | 455123 | 455833 | F | dnaQ_1-DNA Pol III Epsilon Chain_1-(CT261) |
| CPn0411 | 455833 | 456609 | F | CT262 hypothetical protein |
| CPn0412 | 456590 | 457246 | F | CT263 hypothetical protein |
| CPn0413 | 459203 | 457227 | R | msbA-Transport ATP Binding Protein-(CT264) |
| CPn0414 | 460143 | 459172 | R | accA-AcCoA Carboxylase/Transferase Alpha-(CT265) |
| CPn0415 | 461498 | 460221 | R | CT266 hypothetical protein |
| CPn0416 | 461856 | 461557 | R | himD/ihfA-Integration Host Factor Alpha-(CT267) |
| CPn0417 | 463035 | 462244 | R | amiA-N-Acetylmuramoyl Alanine Amidase-(CT268) |
| CPn0418 | 464401 | 462953 | R | murE-N-Acetylmuramoylalanylglutamyl DAP Ligase-(CT269) |
| CPn0419 | 466834 | 464876 | R | pbp3-transglycolase/transpeptidase-(CT270) |
| CPn0420 | 467108 | 466824 | R | CT271 hypothetical protein |
| CPn0421 | 467998 | 467108 | R | yabC-PBP2B Family methyltransferase-(CT272) |
| CPn0422 | 468242 | 468784 | F | CT273 hypothetical protein |
| CPn0423 | 468791 | 469216 | F | CT274 hypothetical protein |
| CPn0424 | 469612 | 470961 | F | dnaA_2-Replication Initiation Factor_2-(CT275) |
| CPn0425 | 470980 | 471564 | F | CT276 hypothetical proteins |
| CPn0426 | 472111 | 471536 | R | CT277 similarity |
| CPn0427 | 472207 | 473715 | F | nqr2-NADH (Ubiquinone) Dehydrogenase-(CT278) |
| CPn0428 | 473722 | 474681 | F | nqr3-NADH (Ubiquinone) Oxidoreductase, Gamma-(CT279) |
| CPn0429 | 474681 | 475319 | F | nqr4-NADH (Ubiquinone) Reductase 4-(CT280) |
| CPn0430 | 475326 | 476093 | F | nqr5-NADH (Ubiquinone) Reductase 5-(CT281) |
| CPn0431 | 476483 | 476151 | R | |
| CPn0432 | 476816 | 476514 | R | |
| CPn0433 | 477273 | 476929 | R | gcsH-Glycine Cleavage System H Protein-(CT282) |
| CPn0434 | 479462 | 477276 | R | CT283 hypothetical protein |
| CPn0435 | 480902 | 479475 | R | Phospholipase D superfamily [uncleavable leader peptide]-(CT284) |
| CPn0436 | 481618 | 480902 | R | lplA-Lipoate Protein Ligase-Like Protein-(CT285) |
| CPn0437 | 481816 | 484350 | F | clpC-ClpC Protease-(CT286) |
| CPn0438 | 485416 | 484334 | R | ycbF-PP-loop superfamily ATPase-(CT287) |
| CPn0439 | 485553 | 486077 | F | |
| CPn0440 | 486105 | 486740 | F | |
| CPn0441 | 486891 | 487838 | F | CT007 hypothetical protein |
| CPn0442 | 488013 | 488528 | F | CT006 hypothetical protein |
| CPn0443 | 488729 | 489979 | F | CT005 hypothetical protein |
| CPn0444 | 490287 | 494507 | F | pmp_6-Polymorphic Outer Membrane Protein G/I Family |
| CPn0445 | 494772 | 497579 | F | pmp_7-Polymorphic Outer Membrane Protein G Family |
| CPn0446 | 497626 | 500415 | F | pmp_8-Polymorphic Outer Membrane Protein G Family |
| CPn0447 | 500568 | 503351 | F | pmp_9-Polymorphic Outer Membrane Protein G/I Family |
| CPn0448 | 504810 | 503698 | R | *yxjG_Bs_2 Hypothetical Protein |
| CPn0449 | 507231 | 505330 | R | pmp_10-PMP_10 (Frame-shift with 0451) |
| CPn0450 | 508112 | 507180 | R | pmp_10-Polymorphic Outer Membrane Protein G Family |
| CPn0451 | 508275 | 511058 | F | pmp_11-Polymorphic Outer Membrane Protein G Family |
| CPn0452 | 511319 | 512860 | F | pmp_12-Polymorphic Outer Membrane Protein A/I Family (truncated) |
| CPn0453 | 513234 | 516152 | F | pmp_13-Polymorphic Outer Membrane Protein G Family |
| CPn0454 | 516182 | 519115 | F | pmp_14-Polymorphic Outer Membrane Protein H Family |
| CPn0455 | 520348 | 519458 | R | |
| CPn0456 | 521532 | 520327 | R | |
| CPn0457 | 523865 | 522120 | R | |
| CPn0458 | 526320 | 524236 | R | |
| CPn0459 | 527005 | 526619 | R | |
| CPn0460 | 527840 | 526992 | R | |
| CPn0461 | 528638 | 527844 | R | |
| CPn0462 | 531052 | 529037 | R | |
| CPn0463 | 532357 | 531191 | R | |
| CPn0464 | 532842 | 532366 | R | |
| CPn0465 | 533212 | 532871 | R | |
| CPn0466 | 533724 | 536537 | F | pmp_15-Polymorphic Outer Membrane Protein E Family |
| CPn0467 | 536633 | 539434 | F | pmp_16-Polymorphic Outer Membrane Protein E Family |
| CPn0468 | 539632 | 540432 | F | pmp_17-Polymorphic Outer Membrane Protein E Family |
| CPn0469 | 540399 | 541460 | F | pmp_17-Polymorphic Outer Membrane Protein (Frame-shift with 0469) |
| CPn0470 | 541357 | 542532 | F | pmp_17-Polymorphic Outer Membrane Protein (Frame-shift with 0470) |
| CPn0471 | 542564 | 545401 | F | pmp_18-Polymorphic Outer Membrane Protein E/F Family |
| CPn0472 | 547905 | 545581 | R | |
| CPn0473 | 549593 | 548070 | R | |
| CPn0474 | 551573 | 549807 | R | CT365 hypothetical protein |
| CPn0475 | 553844 | 551685 | R | glgB-Glucan Branching Enzyme-(CT866) |
| CPn0476 | 554844 | 553858 | R | CT865 hypothetical protein |
| CPn0477 | 556106 | 554844 | R | *yqeV_Bs Hypothetical Protein |
| CPn0478 | 557625 | 556210 | R | hflX-GTP Binding Protein-(CT379) |
| CPn0479 | 558425 | 557616 | R | phnP-Metal Dependent Hydrolase-(CT380) |
| CPn0480 | 559303 | 558650 | R | CT383 hypothetical protein |
| CPn0481 | 560946 | 559339 | R | |
| CPn0482 | 561737 | 560961 | R | artJ-Arginine Periplasmic Binding Protein-(CT381) |
| CPn0483 | 561836 | 564964 | F | |
| CPn0484 | 564970 | 565824 | F | aroG-Deoxyheptonate Aldolase-(CT382) |
| CPn0485 | 566038 | 566229 | F | CT382.1 hypothetical protein |
| CPn0486 | 567784 | 566405 | R | *hypothetical proline permease |
| CPn0487 | 569740 | 568112 | R | CT384 hypothetical protein |
| CPn0488 | 570096 | 569767 | R | hitA-HIT Family Hydrolase-(CT385) |
| CPn0489 | 570965 | 570096 | R | CT386 hypothetical protein |
| CPn0490 | 571279 | 573333 | F | CT387 hypothetical protein |
| CPn0491 | 574352 | 573336 | R | CT389 hypothetical protein |
| CPn0492 | 574652 | 574804 | F | |
| CPn0493 | 575004 | 574855 | R | |
| CPn0494 | 575364 | 575146 | R | |
| CPn0495 | 575603 | 576793 | F | aspC-Aspartate Aminotransferase-(CT390) |
| CPn0496 | 576793 | 577812 | F | CT391 hypothetical protein |
| CPn0497 | 578089 | 577820 | R | CT388 hypothetical protein |
| CPn0498 | 579035 | 578085 | R | |
| CPn0499 | 580359 | 579205 | R | |
| CPn0500 | 580659 | 582362 | F | proS-Prolyl tRNA Synthetase-(CT393) |
| CPn0501 | 582457 | 583650 | F | hrcA-HTH Transcriptional Repressor-(CT394) |
| CPn0502 | 583650 | 584201 | F | grpE-HSP-70 Cofactor-(CT395) |
| CPn0503 | 584234 | 586213 | F | dnaK-HSP-70-(CT396) |
| CPn0504 | 586487 | 588514 | F | vacB-ribonuclease family-(CT397) |
| CPn0505 | 588519 | 589106 | F | *3-methyladenine DNA glycosylase |
| CPn0506 | 589172 | 589840 | F | CT421 hypothetical protein |
| CPn0507 | 589961 | 590122 | F | CT421.1 hypothetical protein |
| CPn0508 | 590142 | 590300 | F | CT421.2 hypothetical protein |
| CPn0509 | 590335 | 590808 | F | (predicted Metalloenzyme)-(CT422) |
| CPn0510 | 590813 | 591973 | F | tlyC_2-CBS Domains (Hemolysin homolog)_2-(CT423) |
| CPn0511 | 592141 | 592488 | F | rsbV_1-Sigma Regulatory Factor_1-(CT424) |
| CPn0512 | 592553 | 594412 | F | CT425 hypothetical protein |
| CPn0513 | 594647 | 595753 | F | Fe--S oxidoreductase_1-(CT426) |
| CPn0514 | 595729 | 596520 | F | CT427 hypothetical protein |
| CPn0515 | 596492 | 597181 | F | ubiE-Ubiquinone Methyltransferase-(CT428) |
| CPn0516 | 598814 | 597255 | R | |
| CPn0517 | 599631 | 598795 | R | |
| CPn0518 | 600803 | 599832 | R | CT429 hypothetical protein |
| CPn0519 | 601674 | 600904 | R | dapF-Diaminopimelate Epimerase-(CT430) |
| CPn0520 | 602218 | 601646 | R | clpP-CLP Protease-(CT431) |
| CPn0521 | 603797 | 602241 | R | glyA-Serine Hydroxymethyltransferase-(CT432) |
| CPn0522 | 603987 | 604655 | F | CT433 hypothetical protein |
| CPn0523 | 604723 | 605052 | F | |
| CPn0524 | 605103 | 606179 | F | |
| CPn0525 | 606522 | 607283 | F | CT398 hypothetical protein |
| CPn0526 | 608696 | 607710 | R | yrbH-GutQ/KpsF Family Sugar-P Isomerase-(CT399) |
| CPn0527 | 609904 | 608726 | R | sucB_2-Dihydrolipoamide Succinyltransferase_2-(CT400) |
| CPn0528 | 611162 | 609921 | R | gltT-Glutamate Symport-(CT401) |
| CPn0529 | 612259 | 611165 | R | ycaH-ATPase-(CT402) |
| CPn0530 | 613254 | 612460 | R | spoU_1-rRNA Methylase_1-(CT403) |
| CPn0531 | 614069 | 613245 | R | SAM dependent methyltransferase-(CT404) |
| CPn0532 | 614674 | 614075 | R | ribC/risA-Riboflavin Synthase-(CT405) |
| CPn0533 | 614930 | 615385 | F | CT406 hypothetical protein |
| CPn0534 | 615413 | 615784 | F | dksA-DnaK Suppressor-(CT407) |
| CPn0535 | 615793 | 616296 | F | lspA-Lipoprotein Signal Peptidase-(CT408) |
| CPn0536 | 616345 | 617691 | F | dagA_1-D-Ala/Gly Permease_1-(CT409) |
| CPn0537 | 617833 | 618189 | F | CT814.1 hypothetical protein |
| CPn0538 | 618212 | 618511 | F | CT814 hypothetical protein |
| CPn0539 | 618705 | 621545 | F | pmp_19-polymorphic outer membrane protein A Family-(CT412) |
| CPn0540 | 621694 | 626862 | F | pmp_20-polymorphic outer membrane protein B Family-(CT413) |
| CPn0541 | 627170 | 628003 | F | Solute binding protein (-yebL-Synechocystis Adhesin Homolog)-(CT415) |
| CPn0542 | 628003 | 628737 | F | ABC Transporter ATPase-(CT416) |
| CPn0543 | 628725 | 629603 | F | (Metal Transport Protein)-(CT417) |
| CPn0544 | 630529 | 629525 | R | yhbZ-GTP binding protein-(CT418) |
| CPn0545 | 630884 | 630633 | R | rl27-L27 ribosomal protein-(CT419) |
| CPn0546 | 631229 | 630912 | R | rl21-L21 Robosomal Protein-(CT420) |
| CPn0547 | 631661 | 632188 | F | ygbB family-(CT434) |
| CPn0548 | 633231 | 632191 | R | cysJ-Sulfite Reductase-(CT435) |
| CPn0549 | 633569 | 633255 | R | rs10-S10 Ribosomal Protein-(CT436) |
| CPn0550 | 635661 | 633580 | R | fusA-Elongation Factor G-(CT437) |
| CPn0551 | 636168 | 635598 | R | rs7-S7 Ribosomal Protein-(CT438) |
| CPn0552 | 636587 | 636219 | R | rs12-S12 Ribosomal Protein (CT439) |
| CPn0553 | 637747 | 636812 | R | |
| CPn0554 | 637854 | 638141 | F | CT440 hypothetical protein |
| CPn0555 | 638298 | 640241 | F | tsp-Tail-Specific Protease-(CT441) |
| CPn0556 | 640912 | 640325 | R | crpA-15 kDa Cysteine-Rich Protein-(CT442) |
| CPn0557 | 642861 | 641194 | R | omcB-60 kDa Cysteine-Rich Outer Membrane Complex Protein-(CT443) |
| CPn0558 | 643300 | 643031 | R | omcA-9 kDa-Cysteine-Rich Outer Membrane Complex Lipoprotein-(CT444) |
| CPn0559 | 643742 | 643927 | F | CT441.1 hypothetical protein |
| CPn0560 | 645612 | 644098 | R | gltX-Glutamyl-tRNA Synthetase-(CT445) |
| CPn0561 | 646404 | 645871 | R | euo-CHLPS Euo Protein-(CT446) |
| CPn0562 | 648036 | 646918 | R | *CHLPS 43 kDa protein homolog_1 |
| CPn0563 | 650056 | 648293 | R | recJ-ssDNA Exonuclease-(CT447) |
| CPn0564 | 654350 | 650145 | R | secD&secF-Protein Export Proteins SecD/SecF (fusion)-(CT448) |
| CPn0565 | 655630 | 654533 | R | CT449 hypothetical protein |
| CPn0566 | 656141 | 656890 | F | yaeS family-(CT450) |
| CPn0567 | 656894 | 657817 | F | cdsA-Phosphatidate Cytidylytransferase-(CT451) |
| CPn0568 | 657817 | 658464 | F | cdsA-Phosphatidate Cytidylytransferase-(CT452) |
| CPn0569 | 658464 | 659099 | F | plsC-Glycerol-3-P Acyltransferase-(CT453) |
| CPn0570 | 659107 | 660789 | F | argS-Arginyl tRNA Transferase-(CT454) |
| CPn0571 | 662122 | 660749 | R | murA-UDP-N-Acetylglucosamine Transferase-(CT455) |
| CPn0572 | 662352 | 664616 | F | CT456 hypothetical protein |
| CPn0573 | 665404 | 664691 | R | yebC family-(CT457) |
| CPn0574 | 665945 | 665394 | R | |
| CPn0575 | 666494 | 665982 | R | YhhY-Amino Group Acetyl Transferase-(CT458) |
| CPn0576 | 667543 | 666494 | R | prfB-Peptide Chain Release Factor 2 (natural UGA frame-shift)-(CT455) |
| CPn0576 | 667598 | 667530 | R | prfB-(natural UGA frame-shift) |
| CPn0577 | 667895 | 668155 | F | SWIB (YM74) complex protein-(CT460) |
| CPn0578 | 668406 | 669365 | F | yaeI-phosphohydrolase-(CT461) |
| CPn0579 | 669361 | 669993 | F | ygbP/yacM-Sugar Nucleotide Phosphorylase-(CT462) |
| CPn0580 | 669993 | 670793 | F | truA-Pseudouridylate Synthase I-(CT463) |
| CPn0581 | 671434 | 670745 | R | Phosphoglycolate Phosphatase-(CT464) |
| CPn0582 | 671503 | 672177 | F | CT465 hypothetical protein |
| CPn0583 | 672400 | 672717 | F | CT466 hypothetical protein |
| CPn0584 | 672707 | 673798 | F | atoS/ntrB-2-Component Sensor-(CT467) |
| CPn0585 | 675817 | 673865 | R | *similarity to Cps IncA_2 |
| CPn0586 | 676026 | 677183 | F | atoC/ntrC-2-Component Regulator-(CT468) |
| CPn0587 | 677441 | 678124 | F | *yvyD_Bs conserved hypothetical protein |
| CPn0588 | 678084 | 678626 | F | CT469 hypothetical protein |
| CPn0589 | 678640 | 679395 | F | CT470 hypothetical protein |
| CPn0590 | 680112 | 679516 | F | CT471 hypothetical protein |
| CPn0591 | 680373 | 681020 | F | yagE family-(CT472) |
| CPn0592 | 681153 | 681461 | R | yidD family-(CT473) |
| CPn0593 | 682476 | 681391 | R | CT474 hypothetical protein |
| CPn0594 | 682583 | 684958 | F | pheT-phenylalanyl tRNA Synthetase Beta-(CT475) |
| CPn0595 | 684958 | 685926 | R | CT476 hypothetical protein |
| CPn0596 | 685939 | 686457 | F | ada-methyltransferase-(CT477) |
| CPn0597 | 688215 | 686479 | R | oppC_2-Oligopeptide Permease_2-(CT478) |
| CPn0598 | 689697 | 688219 | R | oppB_2-Oligopeptide Permease_2-(CT479) |
| CPn0599 | 691802 | 689682 | R | oppA_5-oligopeptide Binding Lipoprotein_5-(CT480) |
| CPn0600 | 692147 | 691827 | R | |
| CPn0601 | 693053 | 692736 | R | CT483 hypothetical protein |
| CPn0602 | 694105 | 693104 | R | CT484 hypothetical protein |
| CPn0603 | 694205 | 695185 | F | hemZ-Ferrochetalase-(CT485) |
| CPn0604 | 695945 | 695196 | R | fliY-Glutamine Binding Protein-(CT486) |
| CPn0605 | 696707 | 696150 | R | yhhF-Methylase-(CT487) |
| CPn0606 | 697444 | 696707 | R | CT488 hypothetical protein |
| CPn0607 | 698895 | 697573 | R | glgC-Glucose-1-P Adenyltransferase-(CT489) |
| CPn0608 | 699645 | 699016 | R | *pyrF-Uridine 5'-Monophosphate Synthase (Ump Synthase)-truncated? |
| CPn0609 | 699705 | 699986 | F | CT490 hypothetical protein |
| CPn0610 | 701420 | 700029 | R | rho-Transcription Termination Factor-(CT491) |
| CPn0611 | 702025 | 701420 | R | yacE-predicted phosphatase/kinase-(CT492) |
| CPn0612 | 704631 | 702022 | R | polA-DNA Polymerase I-(CT493) |
| CPn0613 | 705656 | 704658 | R | sohB-Protease-(CT494) |
| CPn0614 | 707402 | 705783 | R | adt_2-ADP/ATP Translocase_2-(CT495) |
| CPn0615 | 708137 | 707634 | R | pgsA_1-Glycerol-3-P Phosphatidyltransferase_1-(CT496) |
| CPn0616 | 708791 | 710137 | F | dnaB-Replicative DNA Helicase-(CT497) |
| CPn0617 | 710484 | 712316 | F | gidA-FAD-dependent oxidoreductase-(CT498) |
| CPn0618 | 712306 | 713010 | F | lplA-Lipoate-Protein Ligase A-(CT499) |
| CPn0619 | 713444 | 713013 | R | ndk-Nucleoside-2-P Kinase-(CT500) |
| CPn0620 | 714139 | 713519 | R | ruvA-Holliday Junction Helicase-(CT501) |
| CPn0621 | 714647 | 714144 | R | ruvC-Crossover Junction Endonuclease-(CT502) |
| CPn0622 | 715752 | 714793 | R | CT503 hypothetical protein |
| CPn0623 | 716993 | 716163 | R | CT504 hypothetical protein |
| CPn0624 | 718015 | 717011 | R | gapA-Glyceraldehyde-3-P Dehydrogenase-(CT505) |
| CPn0625 | 718485 | 718060 | R | rl17-L17 Ribosomal Protein-(CT506) |
| CPn0626 | 719616 | 718495 | R | rpoA-RNA Polymerase Alpha-(CT507) |
| CPn0627 | 720038 | 719640 | R | rs11-S11 Ribosomal Protein-(CT508) |
| CPn0628 | 720428 | 720063 | R | rs13-S13 Ribosomal Protein-(CT509) |
| CPn0629 | 721857 | 720487 | R | secY-Translocase-(CT510) |
| CPn0630 | 722316 | 721885 | R | rl15-L15 Ribosomal Protein-(CT511) |
| CPn0631 | 722806 | 722312 | R | rs5-S5 Ribosomal Protein-(CT512) |
| CPn0632 | 723195 | 722827 | R | rl18-L18 Ribosomal Protein-(CT513) |
| CPn0633 | 723757 | 723209 | R | rl6-L6 Ribosomal Protein-(CT514) |
| CPn0634 | 724185 | 723787 | R | rs8-S8 Ribosomal Protein-(CT515) |
| CPn0635 | 724745 | 724206 | R | rl5-L5 Ribosomal Protein-(CT516) |
| CPn0636 | 725082 | 724750 | R | rl24-L24 Ribosomal Protein-(CT517) |
| CPn0637 | 725464 | 725099 | R | rl14-L14 Ribosomal Protein-(CT518) |
| CPn0638 | 725747 | 725490 | R | rs17-S17 Ribosomal Protein-(CT519) |
| CPn0639 | 725958 | 725743 | R | rl29-L29 Ribosomal Protein-(CT520) |
| CPn0640 | 726377 | 725964 | R | rl16-L16 Ribosomal Protein-(CT521) |
| CPn0641 | 727077 | 726409 | R | rs3-S3 Ribosomal Protein-(CT522) |
| CPn0642 | 727428 | 727096 | R | rl22-L22 Ribosomal Protein-(CT523) |
| CPn0643 | 727713 | 727450 | R | rs19-S19 Ribosomal Protein-(CT524) |
| CPn0644 | 728573 | 727722 | R | rl2-L2 Ribosomal Protein-(CT525) |
| CPn0645 | 728930 | 728598 | R | rl23-L23 Ribosomal Protein-(CT526) |
| CPn0646 | 729621 | 728950 | R | rl4-L4 Ribosomal Protein-(CT527) |
| CPn0647 | 730331 | 729657 | R | rl3-L3 Ribosomal Protein-(CT528) |
| CPn0648 | 731603 | 730605 | R | CT529 hypothetical protein |
| CPn0649 | 732672 | 731710 | R | fmt-Methionyl tRNA Formyltransferase-(CT530) |
| CPn0650 | 733501 | 732665 | R | lpxA-Acyl-Carrier UDP-GlcNAc-(CT531) |
| CPn0651 | 733975 | 733517 | R | fabZ-Myristoyl-Acyl Carrier Dehydratase-(CT532) |
| CPn0652 | 734835 | 733990 | R | lpxC-Myristoyl GlcNac Deacetylase-(CT533) |
| CPn0653 | 736490 | 734868 | R | cutE-Apolipoprotein N-Acetyltransferase-(CT534) |
| CPn0654 | 736967 | 736503 | R | vdlD/yciA-acyl-CoA Thioesterase-(CT535) |
| CPn0655 | 737847 | 737101 | R | dnaQ_2-DNA Pol III Epsilon Chain_2-(CT536) |
| CPn0656 | 737872 | 738048 | F | |
| CPn0657 | 738473 | 738051 | R | yjeE (ATPase or Kinase)-(CT537) |
| CPn0658 | 739168 | 738455 | R | CT538 hypothetical protein |
| CPn0659 | 739533 | 739838 | F | trxA-Thioredoxin-(CT539) |
| CPn0660 | 740327 | 739860 | R | spoU_2-rRNA Methylase_2-(CT540) |
| CPn0661 | 741100 | 740327 | R | mip-FKBP-type peptidyl-prolyl cis-trans isomerase-(CT541) |
| CPn0662 | 742923 | 741172 | R | aspS-Aspartyl tRNA Synthetase-(CT542) |
| CPn0663 | 744190 | 742901 | R | hisS-Histidyl tRNA Synthetase-(CT543) |
| CPn0664 | 744757 | 744557 | R | |
| CPn0665 | 745001 | 746365 | F | uhpC-Hexosphosphate Transport-(CT544) |
| CPn0666 | 746388 | 750107 | F | dnaE-DNA Pol III Alpha-(CT545) |
| CPn0667 | 751058 | 750177 | R | predicted OMP (leader (17)-(CT546) |
| CPn0668 | 751209 | 752162 | F | CT547 hypothetical protein |
| CPn0669 | 752179 | 752775 | F | CT548 hypothetical protein |
| CPn0670 | 752765 | 753196 | F | rsbW-sigma regulatory factor-histidine kinase-(CT549) |
| CPn0671 | 753630 | 753205 | R | CT550 hypothetical protein |
| CPn0672 | 753741 | 755048 | F | dacF(pbpS)-D-Ala-D-Ala Caroxypeptidase-(CT551) |
| CPn0673 | 755287 | 755463 | F | CT552 hypothetical protein |
| CPn0674 | 756668 | 755577 | R | fmu-RNA Methyltransferase-(CT553) |
| CPn0675 | 757919 | 756768 | R | CT696 hypothetical protein |
| CPn0676 | 759217 | 758051 | R | homologous to CT695 |
| CPn0677 | 760401 | 759256 | R | |
| CPn0678 | 761320 | 760682 | R | |
| CPn0679 | 762930 | 761725 | R | pgk-Phosphoglycerate Kinase-(CT693) |
| CPn0680 | 764248 | 762971 | R | ygo4-Phosphate Permease-(CT692) |
| CPn0681 | 764929 | 764258 | R | CT691 hypothetical protein |
| CPn0682 | 764984 | 765955 | F | dppD-ABC ATPase Dipeptide Transport-(CT690) |
| CPn0683 | 765948 | 766919 | F | dppF-ABC ATPase Dipeptide Transport-(CT689) |
| CPn0684 | 768038 | 767181 | R | spoJ/parB-Chromosome Partitioning Protein-(CT688) |
| CPn0685 | 768068 | 768217 | F | |
| CPn0686 | 768361 | 768176 | R | |
| CPn0687 | 768564 | 769214 | F | CT482 hypothetical protein |
| CPn0688 | 769382 | 770137 | F | CT481 hypothetical protein |
| CPn0689 | 771404 | 770187 | R | yfhO_1-NifS-related Aminotransferase_1-(CT687) |
| CPn0690 | 772680 | 771436 | R | ABC Transporter Membrane Protein-(CT686) |
| CPn0691 | 773452 | 772685 | R | abcX-ABC Transporter ATPase-(CT685) |
| CPn0692 | 774912 | 773461 | R | ABC Transporter-(CT684) |
| CPn0693 | 776256 | 775240 | R | TPR Repeats (O-Linked GlcNAc Transferase similarity)-(CT683) |
| CPn0694 | 779599 | 776330 | R | pbp2-PBP2-transglycolase/transpeptidase-(CT682) |
| CPn0695 | 780216 | 781382 | F | ompA-Major Outer Membrane Protein-(CT681) |
| CPn0696 | 781769 | 782599 | F | rs2-S2 Ribosomal Protein-(CT680) |
| CPn0697 | 782602 | 783447 | F | tsf-Elongation Factor T5-(CT679) |
| CPn0698 | 783458 | 784201 | F | pyrH-UMP Kinase-(CT679) |
| CPn0699 | 784182 | 784721 | F | rrf-Ribosome Releasing Factor-(CT677) |
| CPn0700 | 785097 | 785609 | F | CT676 hypothetical protein |
| CPn0701 | 785599 | 786672 | F | karG-Arginine Kinase-(CT675) |
| CPn0702 | 789685 | 786929 | R | yscC/gspD-Yop C/Gen Secretion Protein D-(CT674) |
| CPn0703 | 791190 | 789685 | R | pkn5-S/T Protein Kinase-(CT673) |
| CPn0704 | 792321 | 791209 | R | fliN-Flagellar Motor Switch Domain/YacQ family-(CT672) |
| CPn0705 | 793173 | 792334 | R | CT671 hypothetical protein |
| CPn0706 | 793683 | 793180 | R | CT670 hypothetical protein |
| CPn0707 | 795029 | 793704 | R | yscN-Yop N (Flagellar-Type ATPase)-(CT669) |
| CPn0708 | 795705 | 795034 | R | CT668 hypothetical protein |
| CPn0709 | 796188 | 795742 | R | CT667 hypothetical protein |
| CPn0710 | 796461 | 796210 | R | CT666 hypothetical protein |
| CPn0711 | 796731 | 796486 | R | CT665 hypothetical protein |
| CPn0712 | 799315 | 796781 | R | FHA domain: homology to adenylate cyclase)-(CT664) |
| CPn0713 | 799721 | 799332 | R | CT663 hypothetical protein |
| CPn0714 | 801107 | 800091 | R | hemA-Glutamyl tRNA Reductase-(CT662) |
| CPn0715 | 801657 | 803462 | F | gyrB_2-DNA Gyrase Subunit B_2-(CT661) |
| CPn0716 | 803469 | 804902 | F | gyrA_2-DNA Gyrase Subunit A_2-(CT660) |
| CPn0717 | 805010 | 805306 | F | CT656 hypothetical protein |
| CPn0718 | 805309 | 805626 | F | CT657 hypothetical protein |
| CPn0719 | 805916 | 806890 | F | sfhB-(Pseudouridine Synthase)-(CT658) |
| CPn0720 | 807003 | 807236 | F | CT659 hypothetical protein |
| CPn0721 | 807683 | 808489 | F | kdsA-KDO Synthetase-(CT655) |
| CPn0722 | 808489 | 808974 | F | CT654 hypothetical protein |
| CPn0723 | 808984 | 809703 | F | yhbG-ABC Transporter ATPase-(CT653) |
| CPn0724 | 810527 | 809706 | R | |
| CPn0725 | 810811 | 810587 | R | CT652.1 hypothetical protein |
| CPn0726 | 813372 | 810880 | R | CT620 hypothetical protein |
| CPn0727 | 813577 | 816192 | F | CT619 hypothetical protein |
| CPn0728 | 818477 | 816525 | R | CHLPN 76 kDa Homolog_1 (CT622) |
| CPn0729 | 819857 | 818592 | R | CHLPN 76 kDa Homolog_2 (CT623) |
| CPn0730 | 821603 | 819963 | R | mviN-Integral Membrane Protein-(CT624) |
| CPn0731 | 821587 | 821760 | F | |
| CPn0732 | 822098 | 822976 | F | nfo-Endonuclease IV-(CT625) |
| CPn0733 | 823727 | 823101 | R | rs4-S4 Ribosomal Protein-(CT626) |
| CPn0734 | 823944 | 824915 | F | yceA-(CT627) |
| CPn0735 | 825668 | 825003 | R | *pyrH/udk-Uridine Kinase (Uridine Monophosphokinase) (Pyrimidine |
| Ribonucleoside Kinase) | ||||
| CPn0736 | 827686 | 825992 | R | ygeD-Efflux Protein-(CT641) |
| CPn0737 | 827685 | 830756 | F | recC-Exodeoxyribonuclease V, Gamma-(CT640) |
| CPn0738 | 830746 | 833895 | F | recB-Exodeoxyribonuclease V, Beta-(CT639) |
| CPn0739 | 834871 | 833861 | R | CT638 hypothetical protein |
| CPn0740 | 836048 | 834864 | R | tyrB-Aromatic AA Aminotransferase-(CT637) |
| CPn0741 | 838350 | 836185 | R | greA-Transcription Elongation Factor-(CT636) |
| CPn0742 | 838463 | 838888 | F | CT635 hypothetical protein |
| CPn0743 | 838962 | 840362 | F | nqrA-Ubiquinone Oxidoreductase, Alpha-(CT634) |
| CPn0744 | 841384 | 840389 | R | hemB-Porphobilinogen Synthase-(CT633) |
| CPn0745 | 841903 | 841742 | R | |
| CPn0746 | 841975 | 843567 | F | CT632 hypothetical protein |
| CPn0747 | 843675 | 843740 | F | CT631 hypothetical protein |
| CPn0747 | 843725 | 843910 | F | CT631 hypothetical protein (frame-shift) |
| CPn0748 | 844987 | 844121 | R | ispA-Geranyl Transtransferase-(CT628) |
| CPn0749 | 845629 | 845006 | R | glmU-UDP-GlcNAc Pyrophosphorylase-(CT629) |
| CPn0750 | 846411 | 845707 | R | tctD/cpxR-HTH Transcriptional Regulatory Protein + Receiver Doman-(CT630) |
| CPn0751 | 846608 | 848434 | F | CT651 hypothetical protein |
| CPn0752 | 848604 | 850082 | F | recD_2-Exodeoxyribonuclease V, Alpha_2-(CT652) |
| CPn0753 | 851006 | 850161 | R | |
| CPn0754 | 851336 | 851040 | R | rs20-S20 Ribosomal Protein-(CT617) |
| CPn0755 | 851597 | 852799 | F | CT616 hypothetical protein |
| CPn0756 | 852961 | 854676 | F | rpoD-RNA Polymerase Sigma-66-(CT615) |
| CPn0757 | 854733 | 855134 | F | folX-Dihydroneopterin Aldolase-(CT614) |
| CPn0758 | 855110 | 856459 | F | folP/dhpS-Dihydropteroate Synthase-(CT613) |
| CPn0759 | 856488 | 856997 | F | folA-Dihydrofolate Reductase-(CT612) |
| CPn0760 | 856957 | 857694 | F | CT611 hypothetical protein |
| CPn0761 | 857704 | 858375 | F | CT610 hypothetical protein |
| CPn0762 | 859597 | 858539 | R | recA-RecA recombination protein-(CT650) |
| CPn0763 | 860511 | 859972 | R | ygfA-Formyltetrahydrofolate Cycloligase-(CT649) |
| CPn0764 | 861807 | 860524 | R | CT648 hypothetical protein |
| CPn0765 | 862382 | 861801 | R | CT647 hypothetical protein |
| CPn0766 | 863782 | 862394 | R | CT646 hypothetical protein |
| CPn0767 | 863884 | 864177 | F | CT645 hypothetical protein |
| CPn0768 | 864159 | 865163 | F | yohI/nir3-predicted oxidoreductase-(CT644) |
| CPn0769 | 867733 | 865121 | R | topA-DNA Topoisomerase I-Fused to SWI Domain-(CT643) |
| CPn0770 | 868340 | 869131 | F | CT642 hypothetical protein |
| CPn0771 | 870463 | 869144 | R | rpoN-RNA Polymerase Sigma-54-(CT609) |
| CPn0772 | 872385 | 870469 | R | uvrD-DNA Helicase-(CT608) |
| CPn0773 | 872488 | 873195 | F | ung-Uracil DNA Glycosylase-(CT607) |
| CPn0774 | 873195 | 873425 | F | CT606.1 hypothetical protein |
| CPn0775 | 874031 | 873414 | R | yggV family-(CT606) |
| CPn0776 | 874246 | 875487 | F | CT605 hypothetical protein |
| CPn0777 | 875601 | 877178 | F | groEL_2-heat shock protein-60-(CT604) |
| CPn0778 | 877505 | 878092 | F | tsa/ahpC-Thio-specific Antioxidant (TSA) Peroxidase-(CT603) |
| CPn0779 | 878481 | 878095 | R | CT602 hypothetical protein |
| CPn0780 | 879205 | 878591 | R | papQ/amiB-N-Acetylmuramoyl-L-Ala Amidase-(CT601) |
| CPn0781 | 879773 | 879198 | R | pal-Peptidoglycan-Associated Lipoprotein-(CT600) |
| CPn0782 | 881065 | 879773 | R | tolB-polysaccharide transporter-(CT599) |
| CPn0783 | 881885 | 881100 | R | CT598 hypothetical protein |
| CPn0784 | 882296 | 881892 | R | exbD-Biopolymer Transport Protein-(CT597) |
| CPn0785 | 882991 | 882296 | R | exbB/tolQ-polysaccharide transporter-(CT596) |
| CPn0786 | 883185 | 885293 | F | dsbD/xprA-Thio:disulfide Interchange Protein-(CT595) |
| CPn0787 | 885619 | 886401 | F | yabD/ycfH-PHP superfamily (urease/pyrimidinase) hydrolase-(CT594) |
| CPn0788 | 886542 | 887432 | F | sdhC-Succinate Dehydrogenase-(CT593) |
| CPn0789 | 887439 | 889316 | F | sdhA-Succinate Dehydrogenase-(CT592) |
| CPn0790 | 889330 | 890103 | F | sdhB-Succinate Dehydrogenase-(CT591) |
| CPn0791 | 893050 | 890111 | R | CT590 hypothetical protein |
| CPn0792 | 894919 | 893108 | R | CT589 hypothetical protein |
| CPn0793 | 896823 | 894919 | R | rbsU-sigma regulatory family protein-PP2C phosphatase (RsbW |
| antagonist)-(CT588) | ||||
| CPn0794 | 897174 | 898004 | F | |
| CPn0795 | 898128 | 899195 | F | |
| CPn0796 | 899301 | 901340 | F | |
| CPn0797 | 901600 | 902694 | F | |
| CPn0798 | 902846 | 903856 | F | |
| CPn0799 | 904986 | 903940 | R | |
| CPn0800 | 906532 | 905249 | R | eno-Enolase-(CT587) |
| CPn0801 | 908697 | 906727 | R | uvrB-Exinuclease ABC Subunit B-(CT586) |
| CPn0802 | 909740 | 908709 | R | trpS-Tryptophanyl tRNA Synthetase-(CT585) |
| CPn0803 | 910303 | 909752 | R | CT584 hypothetical protein |
| CPn0804 | 911059 | 910310 | R | gp6D-CHLTR Plasmid Paralog-(CT583) |
| CPn0805 | 911831 | 911067 | R | minD-chromosome partitioning ATPase-CHLTR plasmid protein GP5D-(CT582) |
| CPn0806 | 913771 | 911867 | R | thrS-Threonyl tRNA Synthetase-(CT581) |
| CPn0807 | 913971 | 914879 | F | CT580 hypothetical protein |
| CPn0808 | 916287 | 914956 | R | CT579 hypothetical protein |
| CPn0809 | 917785 | 916307 | R | CT578 hypothetical protein |
| CPn0810 | 918184 | 917825 | R | CT577 hypothetical protein |
| CPn0811 | 918900 | 918208 | R | lcrH_1-Low Ca Response Protein H_1-(CT576) |
| CPn0812 | 919123 | 920862 | F | mutL-DNA Mismatch Repair-(CT575) |
| CPn0813 | 920870 | 921934 | F | pepP-Aminopeptidase P-(CT574) |
| CPn0814 | 922107 | 923357 | F | CT573 hypothetical protein |
| CPn0815 | 923361 | 925622 | F | gspD/pilQ-Gen. Secretion Protein D-(CT572) |
| CPn0816 | 925615 | 927102 | F | gspE-Gen. Secretion Protein E-(CT571) |
| CPn0817 | 927115 | 928287 | F | gspF-Gen. Secretion Protein F-(CT570) |
| CPn0818 | 928314 | 928682 | F | predicted QMP [leader (16) peptide]-(CT569) |
| CPn0819 | 928689 | 929132 | F | CT568 hypothetical protein |
| CPn0820 | 929120 | 929659 | F | CT567 hypothetical protein |
| CPn0821 | 929667 | 930668 | F | CT566 hypothetical protein |
| CPn0822 | 930756 | 931229 | F | CT565 hypothetical protein |
| CPn0823 | 932367 | 931501 | R | yscT/spaR-YopT Translocation T-(CT564) |
| CPn0824 | 932662 | 932378 | R | yscS/fliQ-YopS/fliQ Translocation Protein-(CT563) |
| CPn0825 | 933594 | 932677 | R | yscR-Yop Translocation R-(CT562) |
| CPn0826 | 934310 | 933612 | R | yscL-Yop Translocation L-(CT561) |
| CPn0827 | 935264 | 934434 | R | CT560 hypothetical protein |
| CPn0828 | 936271 | 935267 | R | yscJ-Yop Translocation J-(CT559) |
| CPn0829 | 936744 | 937298 | F | |
| CPn0830 | 937444 | 937959 | F | |
| CPn0831 | 938267 | 938434 | F | |
| CPn0832 | 939747 | 938827 | R | lipA-Lipoate Synthetase-(CT558) |
| CPn0833 | 941129 | 939747 | R | lpdA-Lipoamide Dehydrogenase-(CT557) |
| CPn0834 | 941553 | 942014 | F | CT556 hypothetical protein |
| CPn0835 | 945689 | 942045 | R | mot1_1-SWI/SNF family helicase_1-(CT555) |
| CPn0836 | 946879 | 945722 | R | brnQ-Amino Acid (Branched) Transport-(CT554) |
| CPn0837 | 947771 | 947145 | R | nth-Enodnuclease III-(CT697) |
| CPn0838 | 949106 | 947781 | R | thdF-Thiophene/Furan Oxidation Protein-(CT698) |
| CPn0839 | 949257 | 950159 | F | psdD-Phosphatidylserine Decarboxylase-(CT699) |
| CPn0840 | 950222 | 951544 | F | CT700 hypothetical protein |
| CPn0841 | 951731 | 954640 | F | secA_2-Translocase SecA_2-(CT701) |
| CPn0842 | 954883 | 954710 | R | CT702 hypothetical protein (frame-shift with 0843) |
| CPn0843 | 955191 | 954994 | R | CT702 hypothetical protein |
| CPn0844 | 956730 | 955270 | R | yphC-GTPase/GTP-binding protein-(CT703) |
| CPn0845 | 958079 | 956850 | R | pcnB_1-Poly A Polymerase_1-(CT704) |
| CPn0846 | 959374 | 958112 | R | clpX-CLP Protease ATPase-(CT705) |
| CPn0847 | 959995 | 959387 | R | clpP-CLP Protease Subunit-(CT706) |
| CPn0848 | 961502 | 960177 | R | tig/murI-Trigger Factor-peptidyl-prolyl isomerase-(CT707) |
| CPn0849 | 961788 | 965285 | F | mot1_2-SWI/SNF family helicase_2-(CT708) |
| CPn0850 | 965293 | 966390 | F | mreB-Rod Shape Protein-Sugar Kinase-(CT709) |
| CPn0851 | 966396 | 968195 | F | pckA-Phosphoenolpyruvate Carboxykinase-(CT710) |
| CPn0852 | 968316 | 970613 | F | CT711 hypothetical protein |
| CPn0853 | 970637 | 971803 | F | CT712 hypothetical protein |
| CPn0854 | 972837 | 971806 | R | ompB-Outer Membrane Protein B-(CT713) |
| CPn0855 | 973995 | 972994 | R | gpdA-Glycerol-3-P Dehydrogenase-(CT714) |
| CPn0856 | 975377 | 973995 | R | AgX-1 Homolog-UDP-Glucose Pyrophosphorylase-(CT715) |
| CPn0857 | 975757 | 975392 | R | CT716 hypothetical protein |
| CPn0858 | 977055 | 975757 | R | fliI-Flagellum-specific ATP Synthase-(CT717) |
| CPn0859 | 977588 | 977055 | R | CT718 hypothetical protein |
| CPn0860 | 978630 | 977608 | R | fliF-Flagellar M-Ring Protein-(CT719) |
| CPn0861 | 979722 | 978925 | R | nifU-NifU-related protein-(CT720) |
| CPn0862 | 980873 | 979722 | R | yfhO_2-NifS-related protein_2-(CT721) |
| CPn0863 | 981514 | 980831 | R | pgmA-Phosphoglycerate Mutase-(CT722) |
| CPn0864 | 981670 | 982374 | F | yjbC-predicted pseudouridine synthase-(CT723) |
| CPn0865 | 982418 | 982942 | F | CT724 hypothetical protein |
| CPn0866 | 983491 | 982916 | R | birA-Biotin Synthetase-(CT725) |
| CPn0867 | 983423 | 984667 | F | rodA-Rod Shape Protein-(CT726) |
| CPn0868 | 986643 | 984670 | R | zntA/cadA-Metal Transport P-type ATPase-(CT727) |
| CPn0869 | 987401 | 986658 | R | CT728 hypothetical protein |
| CPn0870 | 988728 | 987448 | R | serS-Seryl tRNA Synthetase_2-(CT729) |
| CPn0871 | 988772 | 989899 | F | ribD-Riboflavin Deaminase-(CT730) |
| CPn0872 | 989963 | 991216 | F | ribA&ribB-GTP Cyclohydratase & DHBP Synthase-(CT731) |
| CPn0873 | 991233 | 991694 | F | ribE-Ribityllumazine Synthase-(CT732) |
| CPn0874 | 993107 | 991749 | F | CT733 hypothetical protein |
| CPn0875 | 993372 | 994022 | F | CT734 hypothetical protein |
| CPn0876 | 994144 | 995517 | F | dagA_2-D-Alanine/Glycine Permease_2-(CT735) |
| CPn0877 | 995533 | 995982 | F | ybcL family-(CT736) |
| CPn0878 | 996654 | 995992 | F | SET Domain protein-(CT737) |
| CPn0879 | 997439 | 996645 | R | yycJ-metal dependent hydrolase-(CT738) |
| CPn0880 | 999861 | 997444 | R | ftsK-Cell Division Protein FtsK-(CT739) |
| CPn0881 | 1005667 | 1006209 | F | |
| CPn0882 | 1006268 | 1007404 | F | |
| CPn0883 | 1008865 | 1007573 | R | dmpP/nqr6-Phenolhydrolase/NADH ubiquinone oxidoreductase-(CT740) |
| CPn0884 | 1009359 | 1009009 | R | CT741 hypothetical protein |
| CPn0885 | 1010635 | 1009433 | R | ygcA-rRNA Methyltransferse-(CT742) |
| CPn0886 | 1011276 | 1010908 | R | hctA-Histone-Like Developmental Protein-(CT743) |
| CPn0887 | 1011692 | 1014157 | F | CHLTR possible phosphoprotein-(CT744) |
| CPn0888 | 1015423 | 1014119 | R | hemG-protoporphyrinogen Oxidase-(CT745) |
| CPn0889 | 1016835 | 1015462 | R | hemN_2-Coproporphyrinogen III Oxidase_2-(CT746) |
| CPn0890 | 1017805 | 1016819 | R | hemE-Uroporphyrinogen Decarboxylase-(CT747) |
| CPn0891 | 1021073 | 1017819 | R | mfd-Transcription-Repair Coupling-(CT748) |
| CPn0892 | 1023661 | 1021046 | R | alaS-Alanyl tRNA Synthetase-(CT749) |
| CPn0893 | 1023894 | 1025888 | F | tktB-Transketolase-(CT750) |
| CPn0894 | 1026766 | 1025888 | R | amn-AMP Nucleosidase-(CT751) |
| CPn0895 | 1026988 | 1027557 | F | efp_2-Elongation Factor P_2-(CT752) |
| CPn0896 | 1027595 | 1027822 | F | CT753 hypothetical protein |
| CPn0897 | 1028737 | 1027853 | R | (possible phosphohydrolase)-(CT754) |
| CPn0898 | 1030460 | 1028904 | R | Mitochondrial HSP60 Chaperonin Homolog-(CT755) |
| CPn0899 | 1030875 | 1032215 | F | murF-Muramoyl-DAP Ligase-(CT756) |
| CPn0900 | 1032235 | 1033281 | F | mraY-Muramoyl-Pentapeptide Transferase-(CT757) |
| CPn0901 | 1033287 | 1034537 | F | murD-Muramoylalanine-Glutamate Ligase-(CT758) |
| CPn0902 | 1034543 | 1035241 | F | nlpD-Muramidase (invasin repeat family)-(CT759) |
| CPn0903 | 1035263 | 1036417 | F | ftsW-Cell Division Protein FtsW-(CT760) |
| CPn0904 | 1036326 | 1037396 | F | murG-Peptidoglycan Transferase-(CT761) |
| CPn0905 | 1037409 | 1039835 | F | murC&ddlA-Muramate-Ala Ligase & D-Ala-D-Alam Ligase-(CT762) |
| CPn0906 | 1040340 | 1039915 | R | CT763 hypothetical protein |
| CPn0907 | 1040780 | 1040445 | R | *cutA Periplasmic Divalent Cation Tolerance Protein CutA (C-Type |
| Cytochrome Biogenesis Protein) | ||||
| CPn0908 | 1041589 | 1040780 | R | CT764 hypothetical protein |
| CPn0909 | 1041637 | 1041966 | F | rsbV_2-Sigma Factor Regulator_2-(CT765) |
| CPn0910 | 1041979 | 1043004 | F | miaA-tRNA Pyrophosphate Transferase-(CT766) |
| CPn0911 | 1044043 | 1042985 | R | Fe--S cluster oxidoreductase_2-(CT767) |
| CPn0912 | 1044129 | 1045760 | F | CT768 hypothetical protein |
| CPn0913 | 1045760 | 1045945 | F | |
| CPn0914 | 1045999 | 1046397 | F | |
| CPn0915 | 1046461 | 1046817 | F | ybeB-iojap superfamily ortholog-(CT769) |
| CPn0916 | 1046837 | 1048084 | F | fabF-Acyl Carrier Protein Synthase-(CT770) |
| CPn0917 | 1048090 | 1048539 | F | hydrolase/phosphatase homolog-(CT771) |
| CPn0918 | 1049223 | 1048579 | R | ppa-Inorganic Pyrophosphatase-(CT772) |
| CPn0919 | 1049378 | 1050430 | F | ldh-Leucine Dehydrogenase-(CT773) |
| CPn0920 | 1051405 | 1050431 | R | cysQ-Sulfite Synthesis/biphosphate phosphatase-(CT774) |
| CPn0921 | 1051535 | 1052293 | F | snGlycerol-3-P Acyltransferase-(CT775) |
| CPn0922 | 1052314 | 1053927 | F | aas-Acylglycerophosphoethanolamine Acyltransferase-(CT776) |
| CPn0923 | 1053984 | 1055093 | F | bioF_1-Oxononanoate Synthase_1-(CT777) |
| CPn0924 | 1057274 | 1055028 | R | priA-Primosomal Protein N'-(CT778) |
| CPn0925 | 1057900 | 1057226 | R | CT779 hypothetical protein |
| CPn0926 | 1058060 | 1058557 | F | Thioredoxin Disulfide Isomerase-(CT780) |
| CPn0927 | 1059809 | 1058670 | R | *CHLPS 43 kDa protein homolog_2 |
| CPn0928 | 1061008 | 1059884 | R | *CHLPS 43 kDa protein homolog_3 |
| CPn0929 | 1062292 | 1061186 | R | *CHLPS 43 kDa protein homolog_4 |
| CPn0930 | 1062857 | 1063330 | F | |
| CPn0931 | 1064138 | 1065718 | F | lysS-Lysyl tRNA Synthetase-(CT781) |
| CPn0932 | 1067142 | 1065721 | R | cysS-Cysteinyl tRNA Synthetase-(CT782) |
| CPn0933 | 1067535 | 1068578 | F | predicted disulfide bond isomerase-(CT783) |
| CPn0934 | 1068942 | 1068526 | R | rnpA-Ribonuclease P Protein Component-(CT784) |
| CPn0935 | 1069091 | 1068957 | R | rl34-L34 Ribosomal Protein-(CT785) |
| CPn0936 | 1069336 | 1069470 | F | rl36-L36 Ribosomal Protein-(CT786) |
| CPn0937 | 1069496 | 1069798 | F | rs14-S14 Ribosomal Protein-(CT787) |
| CPn0938 | 1070322 | 1069849 | R | CT788 hypothetical protein-(leader (60) peptide-periplasmic) |
| CPn0939 | 1070728 | 1071195 | F | CT790 hypothetical protein |
| CPn0940 | 1073012 | 1071204 | R | uvrC-Excinuclease ABC, Subunit C-(CT791) |
| CPn0941 | 1075501 | 1073018 | R | mutS-DNA Mismatch Repair-(CT792) |
| CPn0942 | 1075985 | 1077754 | F | dnaG/priM-DNA Primase-(CT794) |
| CPn0943 | 1077978 | 1078238 | F | CT794.1 hypothetical protein |
| CPn0944 | 1078512 | 1078997 | F | |
| CPn0945 | 1079070 | 1079660 | F | CT795 hypothetical protein |
| CPn0946 | 1082786 | 1079745 | R | glyQ-Glycyl tRNA Synthetase-(CT796) |
| CPn0947 | 1083442 | 1084059 | F | pgsA_2-Glycerol-3-P-Phosphatydyltransferase_2-(CT797) |
| CPn0948 | 1085474 | 1084047 | R | glgA-Glycogen Synthase-(CT798) |
| CPn0949 | 1085929 | 1086483 | F | ccc-General Stress Protein-(CT799) |
| CPn0950 | 1086488 | 1087027 | F | pth-Peptidyl tRNA Hydrolase-(CT800) |
| CPn0951 | 1087122 | 1087457 | F | rs6-S6 Ribosomal Protein-(CT801) |
| CPn0952 | 1087478 | 1087723 | F | rs18-S18 Ribosomal Protein-(CT802) |
| CPn0953 | 1087742 | 1088248 | F | rl9-L9 Ribosomal Protein-(CT803) |
| CPn0954 | 1088286 | 1088708 | F | ychB-Predicted Kinase-(CT804) |
| CPn0955 | 1088612 | 1089175 | F | (frame-shift with 0954) |
| CPn0956 | 1089560 | 1090909 | F | CT805 hypothetical protein |
| CPn0957 | 1093788 | 1090963 | R | ide/ptr-Insulinase family/Protease III-(CT806) |
| CPn0958 | 1094785 | 1093793 | R | plsB-Glycerol-3-P Acyltransferase-(CT807) |
| CPn0959 | 1096343 | 1094799 | R | cafE-Axial Filament Protein-(CT808) |
| CPn0960 | 1096764 | 1097102 | F | CT809 hypothetical protein |
| CPn0961 | 1097118 | 1097297 | F | rl32-L32 Ribosomal Protein-(CT810) |
| CPn0962 | 1097316 | 1098275 | F | plsX-FA/Phospholipid Synthesis Protein-(CT811) |
| CPn0963 | 1098398 | 1103224 | F | pmp_21-Polymorphic Outer Membrane Protein D Family-(CT812) |
| CPn0964 | 1104758 | 1103301 | R | |
| CPn0965 | 1106736 | 1104925 | R | lpxB-Lipid A Disaccharide Synthase-(CT411) |
| CPn0966 | 1108037 | 1106748 | R | pcnB_2-PolyA Polymerase_2-(CT410) |
| CPn0967 | 1108512 | 1109885 | F | mrsA/pgm-Phosphoglucomutase-(CT815) |
| CPn0968 | 1109895 | 1111721 | F | glmS-Glucosamine-Fructose-6-P Aminotransferase-(CT816) |
| CPn0969 | 1111812 | 1112999 | F | 0969-tyrP_1-Tyrosine Transport_1-(CT817) tyrP_1-Tyrosine Transport_1-(CT817) |
| CPn0970 | 1113461 | 1114648 | F | 0970-tyrP_2-Tyrosine Transport_2-(CT818) tyrP_2-Tyrosine Transport_2-(CT818) |
| CPn0971 | 1114702 | 1115415 | F | yccA-Transport Permease-(CT819) |
| CPn0972 | 1116299 | 1115430 | R | ftsY-Cell Division Protein FtsY-(CT820) |
| CPn0973 | 1116370 | 1117527 | F | sucC-Succinyl-CoA Synthetase, Beta-(CT821) |
| CPn0974 | 1117544 | 1118422 | F | sucD-Succinyl-CoA Synthetase, Alpha-(CT822) |
| CPn0975 | 1119104 | 1119637 | F | |
| CPn0976 | 1120082 | 1121185 | F | |
| CPn0977 | 1121371 | 1122402 | F | |
| CPn0978 | 1122665 | 1123693 | F | |
| CPn0979 | 1123980 | 1125443 | F | htrA-DO Serine Protease-(CT823) |
| CPn0980 | 1126982 | 1125504 | R | *similarity to Saccharomyces serevisiae hypothetical 52.9 KD protein |
| CPn0981 | 1127031 | 1129952 | F | Zinc Metalloprotease (insulinase family)-(CT824) |
| CPn0982 | 1131194 | 1129962 | R | yigN family-(CT825) |
| CPn0983 | 1132000 | 1131206 | R | pssA-Glycerol-Serine Phosphatidyltransferase-(CT826) |
| CPn0984 | 1132379 | 1135510 | F | nrdA-Ribonucleoside Reductase, Large Chain-(CT827) |
| CPn0985 | 1135534 | 1136571 | F | nrdB-Ribonucleoside Reductase, Small Chain-(CT828) |
| CPn0986 | 1136724 | 1137395 | F | yggH-predicted rRNA Methylase-(CT829) |
| CPn0987 | 1137516 | 1138115 | F | ytgB-like predicted rRNA methylase-(CT830) |
| CPn0988 | 1138986 | 1138075 | R | murB-UDP-N-Acetylenolpyruvoylglucosamine Reductase-(CT831) |
| CPn0989 | 1139495 | 1139016 | R | CT832 hypothetical protein |
| CPn0990 | 1139883 | 1140440 | F | infC-Initiation Factor 3-(CT833) |
| CPn0991 | 1140421 | 1140612 | F | rl35-L35 Ribosomal Protein-(CT834) |
| CPn0992 | 1140634 | 1140996 | F | rl20-L20 Ribosomal Protein-(CT835) |
| CPn0993 | 1141014 | 1142030 | F | pheS-Phenylalanyl tRNA Synthetase, Alpha-(CT836) |
| CPn0994 | 1142398 | 1144440 | F | CT837 hypothetical protein |
| CPn0995 | 1145512 | 1144415 | R | CT838 hypothetical protein |
| CPn0996 | 1146589 | 1145519 | R | CT839 hypothetical protein |
| CPn0997 | 1146708 | 1147664 | F | mesJ-PP-loop superfamily ATPase-(CT840) |
| CPn0998 | 1147855 | 1150584 | F | ftsH-ATP-dependent zinc protease-(CT841) |
| CPn0999 | 1152847 | 1150766 | R | pnp-Polyribonucleotide Nucleotidyltransferase-(CT842) |
| CPn1000 | 1153157 | 1152891 | R | rs15-S15 Ribosomal Protein-(CT843) |
| CPn1001 | 1153405 | 1153869 | F | yfhC-cytosine deaminase-(CT844) |
| CPn1002 | 1153862 | 1154089 | F | CT845 hypothetical protein |
| CPn1003 | 1154796 | 1154092 | R | CT846 hypothetical protein |
| CPn1004 | 1155397 | 1154879 | R | CT847 hypothetical protein |
| CPn1005 | 1155933 | 1155415 | R | CT848 hypothetical protein |
| CPn1006 | 1156472 | 1155990 | R | CT849 hypothetical protein |
| CPn1007 | 1156689 | 1156907 | F | CT849.1 hypothetical protein |
| CPn1008 | 1156928 | 1158223 | F | CT850 hypothetical protein |
| CPn1009 | 1159058 | 1158186 | R | map-Methionine Aminopeptidase-(CT851) |
| CPn1010 | 1159672 | 1159067 | R | CT852 hypothetical protein |
| CPn1011 | 1160306 | 1159902 | R | CT853 hypothetical protein |
| CPn1012 | 1162193 | 1160421 | R | yzeB-ABC transporter permease-(CT854) |
| CPn1013 | 1162245 | 1163624 | F | fumC-Pumarate Hydratase-(CT855) |
| CPn1014 | 1165426 | 1163732 | R | ychM-Sulfate Transporter-(CT856) |
| CPn1015 | 1165634 | 1166893 | F | CT857 hypothetical protein (possible IM protein) |
| CPn1016 | 1167042 | 1168898 | F | CT858 hypothetical protein |
| CPn1017 | 1169006 | 1169935 | F | lytB-Metalloprotease-(CT859) |
| CPn1018 | 1169898 | 1170629 | F | |
| CPn1019 | 1172128 | 1170638 | R | CT860 hypothetical protein |
| CPn1020 | 1173679 | 1172150 | R | CT861 hypothetical protein |
| CPn1021 | 1174213 | 1173698 | R | lcrH_2-Low Calcium Response_2-(CT862) |
| CPn1022 | 1175673 | 1174216 | R | CT863 hypothetical protein |
| CPn1023 | 1176035 | 1176331 | F | |
| CPn1024 | 1177236 | 1176334 | R | xerD-Integrase/recombinase-(CT864) |
| CPn1025 | 1177302 | 1178879 | F | pgi-Glucose-6-P Isomerase-(CT378) |
| CPn1026 | 1178997 | 1179137 | F | ltuA-(CT377) |
| CPn1027 | 1179175 | 1180755 | F | |
| CPn1028 | 1181016 | 1181999 | F | mdhC-Malate Dehydrogenase-(CT376) |
| CPn1029 | 1182008 | 1182844 | F | |
| CPn1030 | 1183886 | 1182843 | R | predicted D-amino acid dehydrogenase-(CT375) |
| CPn1031 | 1185552 | 1184098 | R | arcD-Arginine/Ornithine Antiporter-(CT374) |
| CPn1032 | 1186150 | 1185566 | R | CT373 hypothetical protein |
| CPn1033 | 1187500 | 1186187 | R | CT372 hypothetical protein |
| CPn1034 | 1188517 | 1187732 | R | Predicted OMP_1 (CT371) [leader (18) peptide] |
| CPn1035 | 1190000 | 1188570 | R | AroE-Shikimate 5-Dehydrogenase-(CT370) |
| CPn1036 | 1191135 | 1189984 | R | AroB-Dehyroquinate Synthase-(CT369) |
| CPn1037 | 1192199 | 1191123 | R | AroC-Chorismate Synthase-(CT368) |
| CPn1038 | 1192726 | 1192199 | R | aroL-Shikimate Kinase II-(CT367) |
| CPn1039 | 1193999 | 1192665 | R | aroA-Phosphoshikimate Vinyltransferase-(CT366) |
| CPn1040 | 1194741 | 1194073 | R | |
| CPn1041 | 1195994 | 1194726 | R | *bioA-Adenosylmethionine-8-Amino-7-Oxononanoate Aminotransferase |
| CPn1042 | 1196590 | 1195934 | R | *bioD-dethiobiotin synthetase |
| CPn1043 | 1197717 | 1196572 | R | bioF_2-Oxononanoate Synthase_2 |
| CPn1044 | 1198691 | 1197699 | R | *bioB-Biotin Synthase |
| CPn1045 | 1199590 | 1198901 | R | *conserved hypothetical bacterial membrane protein |
| CPn1046 | 1200625 | 1199590 | R | *Tryptophan Hyroxylase |
| CPn1047 | 1200552 | 1201343 | F | dapB-Dihydrodipicolinate Reductase-(CT364) |
| CPn1048 | 1201606 | 1202604 | F | asd-Aspartate Dehydrogenase-(CT363) |
| CPn1049 | 1202595 | 1203914 | F | lysC-Aspartokinase III-(CT362) |
| CPn1050 | 1203926 | 1204798 | F | dapA-Dihydrodipicolinate Synthase-(CT361) |
| CPn1051 | 1204962 | 1205270 | F | |
| CPn1052 | 1205417 | 1206169 | F | |
| CPn1053 | 1206153 | 1206701 | F | |
| CPn1054 | 1207034 | 1209466 | F | |
| CPn1055 | 1209694 | 1210521 | F | |
| CPn1056 | 1210527 | 1211228 | F | |
| CPn1057 | 1211497 | 1213596 | F | CT356 hypothetical protein |
| CPn1058 | 1213748 | 1214836 | F | CT355 hypothetical protein |
| CPn1059 | 1214848 | 1215678 | F | kgsA-Dimethyladenosine Transferase-(CT354) |
| CPn1060 | 1217658 | 1215727 | R | dxs/tkt-Transketolase-(CT331) |
| CPn1061 | 1217920 | 1217666 | R | CT330 hypothetical protein |
| CPn1062 | 1219820 | 1218159 | R | xseA-Exodoxyribonuclease VII-(CT329) |
| CPn1063 | 1219951 | 1220712 | F | tpiS-Triosephosphate Isomerase-(CT328) |
| CPn1064 | 1220719 | 1220895 | F | |
| CPn1065 | 1221095 | 1220928 | R | |
| CPn1066 | 1221135 | 1221488 | F | |
| CPn1067 | 1221735 | 1222292 | F | def-Polypeptide Deformylase-(CT353) |
| CPn1068 | 1223258 | 1222365 | R | rnhB_2-Ribonuclease HII_2-(CT008) |
| CPn1069 | 1223513 | 1223941 | F | yfgA-HTH Transcriptional Regulator-(CT009) |
| CPn1070 | 1225511 | 1224144 | R | |
| CPn1071 | 1227324 | 1225885 | R | |
| CPn1072 | 1227969 | 1228835 | F | |
| CPn1073 | 1229011 | 1229832 | F | Predicted OMP_2-(CT371) |
| TABLE 2 | |||
| (Supplemental Data) Functional Assignments of C. pneumoniae Coding Sequences. | |||
| C. trachomatis genes are shown in parentheses. | |||
| Amino Acid Biosynthesis | |||
| Aromatic Family | |||
| 1039 | (CT366) | aroA | Phosphoshikimate Vinyltransferase |
| 1036 | (CT369) | aroB | Dehyroquinate Synthase |
| 1037 | (CT368) | aroC | Chorismate Synthase |
| 1035 | (CT370) | aroE | Shik:mate 5-Dehyrogenase |
| 0484 | (CT382) | aroG | Deoxyheptonate Aldolase |
| 1038 | (CT367) | aroL | Shikimate Kinase II |
| 0740 | (CT637) | tyrB | Aromatic AA Aminotransferase |
| Aspartate Family (lysine) | |||
| 1048 | (CT363) | asd | Aspartate Dehydrogenase |
| 1050 | (CT361) | dapA | Dihydrodipicolinate Synthase |
| 1047 | (CT364) | dapB | Dihydrodipicolinate Reductase |
| 0519 | (CT430) | dapF | Diaminopimelate Epimerase |
| 1049 | (CT362) | lysC | Aspartokinase III |
| Serine Family | |||
| 0433 | (CT282) | gcsH | Glycine Cleavage System H Protein |
| 0521 | (CT432) | glyA | Serine Hydroxymethyltransferase |
| Base & Nucleotide Metabolism | |||
| 0171 | guaA | GMP Synthase | |
| 0172 | guaB | Inosine 5'-Monophosphase Dehydrogenase | |
| 0608 | Uridine 5'-Monophosphate Synthase | ||
| 0735 | Uridine Kinase | ||
| 0244 | (CT128) | adk | Adenylate Kinase |
| 0894 | (CT751) | amn | AMP Nucleosidase |
| 0568 | (CT452) | cmk | CMP Kinase |
| 0392 | (CT039) | dcd | dCTP Deaminase |
| 0059 | (CT292) | dut | dUTP Nucleotidohydrolase |
| 0120 | (CT030) | gmk | GMP Kinase |
| 0619 | (CT500) | ndk | Nucleoside-2-P Kinase |
| 0984 | (CT827) | nrdA | Ribonucleoside Reductase, Large Chain |
| 0985 | (CT828) | nrdB | Ribonucleoside Reductase, Small Chain |
| 0236 | (CT183) | pyrG | CTP Synthetase |
| 0698 | (CT678) | pyrH | UMP Kinase |
| 0273 | (CT188) | tdk | Thymidylate Kinase |
| 0659 | (CT539) | trxA | Thioredoxin |
| 0314 | (CT099) | trxB | Thioredoxin Reductase |
| 1001 | (CT844) | yfbC | Cytosine Deaminase |
| Biosynthesis of Cofactors | |||
| Biotin, Lipoate & Ubiquinone | |||
| 1041 | bioA | Adenosylmethionine-8-Amino-7-Oxononanoate Aminotransferase | |
| 1044 | bioB | Biotin Synthase | |
| 1042 | bioD | Dethiobiotin Synthetase | |
| 0923 | (CT777) | bioF_1 | Oxononanoate Synthase_1 |
| 1043 | (CT777) | bioF_2 | Oxononanoate Synthase_2 |
| 0866 | (CT725) | birA | Biotin Synthetase |
| 0748 | (CT628) | ispA | Geranyl Transtransferase |
| 0832 | (CT558) | lipA | Lipoate Synthetase |
| 0265 | (CT219) | ubiA | Benzoate Octaphenyltransferase |
| 0264 | (CT220) | ubiD | Phenylacrylate Decarboxylase |
| 0515 | (CT428) | ubiE | Ubiquinone Methyltransferase |
| Folic Acid | |||
| 0759 | (CT612) | folA | Dihydrofolate Reductase |
| 0335 | (CT078) | folD | Methylene Tetrahydrofolate Dehydrogenase |
| 0758 | (CT613) | folP | Dihydropteroate Synthase |
| 0757 | (CT614) | folX | Dihydroneopterin Aldolase |
| 0763 | (CT649) | ygfA | Formyltetrahydrofolate Cycloligase |
| Porphyrin | |||
| 0714 | (CT662) | hemA | Glutamyl tRNA Reductase |
| 0744 | (CT633) | hemB | Porphobilinogen Synthase |
| 0052 | (CT299) | hemC | Porphobilinogen Deaminase |
| 0890 | (CT747) | hemE | Uroporphyrinogen Decarboxylase |
| 0888 | (CT745) | hemG | protoporphyrinogen Oxidase |
| 0138 | (CT210) | hemL | Glutamate-1-Semialdehyde-2,1-Aminomutase |
| 0380 | (CT052) | hemN_1 | Coproporphyrinogen III Oxidase_1 |
| 0889 | (CT746) | hemN_2 | Coproporphyrinogen III Oxidase_2 |
| 0603 | (CT485) | hem2 | Ferroehetalase |
| Riboflavin | |||
| 0872 | (CT731) | ribA&ribB | GTP Cyclohydratase & DHBP Synthase |
| 0532 | (CT405) | ribC | Riboflavin Synthase |
| 0871 | (CT730) | ribD | Riboflavin Deaminase |
| 0873 | (CT732) | ribE | Ribityllumazine Synthase |
| 0320 | (CT093) | ribF | FAD Synthase |
| Cell Envelope | |||
| Fatty Acid & Phospholipid Metabolism | |||
| 0161 | (CT206) | (predicted acyltransferase family) | |
| 0922 | (CT776) | aas | Acylglycerophosphoethanolamine Acyltransferase |
| 0414 | (CT265) | accA | AcCoA Carboxylase/Transferase Alpha |
| 0183 | (CT123) | accB | Biotin Carboxyl Carrier Protein |
| 0182 | (CT124) | accC | Biotin Carboxylase |
| 0058 | (CT293) | accD | AcCoA Carboxylase/Transferase Beta |
| 0295 | (CT236) | acpP | Acyl Carrier Protein |
| 0313 | (CT100) | acpS | Acyl-carrier Protein Synthase |
| 0567 | (CT451) | cdsA | Phosphatidate Cytidylytransferase |
| 0297 | (CT238) | fabD | Malonyl Acyl Carrier Transcyclase |
| 0916 | (CT770) | fabF | Acyl Carrier Protein Synthase |
| 0296 | (CT237) | fabG | Oxoacyl (Carrier Protein) Reductase |
| 0298 | (CT239) | fabH | Oxoacyl Carrier Protein Synthase III |
| 0406 | (CT104) | fabI | Enoyl-Acyl-Carrier Protein Reductase |
| 0651 | (CT532) | fabZ | Myrisaoyl-Acyl Carrier Dehydratase |
| 0098 | (CT010) | htrB | Acyltransferase |
| 0271 | (CT136) | Lysophospholipase Esterase | |
| 0615 | (CT496) | pgsA_1 | Glycerol-3-P Phosphatidyltransferase_1 |
| 0947 | (CT797) | pgsA_2 | Glycerol-3-P Phosphatydyltransferase_2 |
| 0958 | (CT807) | plsB | Glycerol-3-P Acyltransferase |
| 0569 | (CT453) | plsC | Glycerol-3-P Acyltransferase |
| 0962 | (CT811) | plsX | FA/Phospholipid Synthesis Protein |
| 0839 | (CT699) | psdD | Phosphatidylserine Decarboxylase |
| 0983 | (CT826) | pssA | Glycerol-Serine Phosphatidyltransferase |
| 0921 | (CT775) | snGlycerol-J-P Acyltransferase | |
| 0654 | (CT535) | yciA | Acyl-CoA Thioesterase |
| 0877 | (CT736) | ybcL | CT736 Hypothetical Protein |
| LPS | |||
| 0154 | (CT208) | gscA | KDO Transferase |
| 0721 | (CT655) | kdsA | KDO Synthetase |
| 0235 | (CT182) | kdsB | Deoxyoctulonosic Acid Synthetase |
| 0650 | (CT531) | lpxA | Acyl-Carrier UDP-GlcNAc O-Acyltransferase |
| 0965 | (CT411) | lpxB | Lipid A Disaccharide Synthase |
| 0652 | (CT533) | lpxC | Myristoyl GlcNac Deacetylase |
| 0302 | (CT243) | lpxD | UDP Glucosamine N-Acyltransferase |
| Membrane Proteins, Lipoproteins & Porins | |||
| 0310 | (CT251) | 60IM | 60 kDa Inner Membrane Protein |
| 0556 | (CT442) | crpA | 15 kDa Cysteine-Rich Protein |
| 0653 | (CT534) | cutE | Apolipoprotein N-Acetyltransferase |
| 0311 | (CT252) | lgt | Prolipoprotein Diacylglycerol Transferase |
| 0558 | (CT444) | omcA | 9 kDa-Cysteine-Rich Lipoprotein |
| 0557 | (CT443) | omcB | 60 kDa Cysteine-Rich OMP |
| 0695 | (CT681) | ompA | Major Outer Membrane Protein |
| 0854 | (CT713) | ompB | Outer Membrane Protein B |
| 0781 | (CT600) | pal | Peptidoglycan-Associated Lipoprotein |
| 0300 | (CT241) | yaeT | Omp85 Homolog |
| Peptidoglycan | |||
| 0417 | (CT268) | amiA | N-Acetylmuramoyl Alanine Amidase |
| 0780 | (CT601) | amiB | N-Acetylmuramoyl-L-Ala Amidase |
| 0672 | (CT551) | dacF | D-Ala-D-Ala Caroxypeptidase |
| 0968 | (CT816) | glmS | Glucosamine-Fructose-6-P Aminotransferase |
| 0749 | (CT629) | glmU | UDP-GlcNAc Pyrophosphorylase |
| 0900 | (CT757) | mrsY | Muramoyl-Pentapeptide Transferase |
| 0571 | (CT455) | murA | UDP-N-Acetylglucosamine Transferase |
| 0988 | (CT831) | murB | UDP-N-Acetylenolpyruvoylglucosamine Reductase |
| 0905 | (CT762) | murC&ddlA | Muramate-Ala Ligase & D-Ala-D-Alam Ligase |
| 0901 | (CT758) | murD | Muramoylalanine-Glutamate Ligase |
| 0418 | (CT269) | murE | N-Acetylmuramoylalanylglutamyl DAP Ligase |
| 0899 | (CT756) | murF | Muramoyl-DAP Ligase |
| 0904 | (CT761) | murG | Peptidoglycan Transferase |
| 0902 | (CT759) | nlpD | Muramidase (invasin repeat family) |
| 0694 | (CT682) | pbp2 | PBP2-Transglycolase/Transpeptidase |
| 0419 | (CT270) | pbp3 | Transglycolase/Transpeptidase |
| 0421 | (CT272) | yabC | PBP2B Family Methyltransferase |
| Cellular Processes | |||
| Cell Division | |||
| 0959 | (CT808) | cafE | Axial Filament Protein |
| 0880 | (CT739) | ftsK | Cell Division Protein FtsK |
| 0903 | (CT760) | ftsW | Cell Division Protein FtsW |
| 0972 | (CT820) | ftsY | Cell Division Protein FtsY |
| 0617 | (CT498) | gidA | FAD-dependent Oxidoreductase |
| 0805 | (CT582) | minD | Chromosome Partitioning ATPase |
| 0850 | (CT709) | mreB | Rod Shape Protein-Sugar Kinase |
| 0867 | (CT726) | rodA | Rod Shape Protein |
| 0684 | (CT688) | parB | Chromosome Partitioning Protein |
| Detoxtification | |||
| 0057 | (CT294) | sodM | Superoxide Dismutase (Mn) |
| 0778 | (CT603) | ahpC | Thio-specific Antioxidant (TSA) Peroxidase |
| Signal Transduction | |||
| 0148 | (CT145) | S/T Protein Kinase | |
| 0584 | (CT467) | asoS | Two-Component Sensor |
| 0294 | (CT235) | cAMP-Dependent Protein Kinase Regulatory Subunit | |
| 0712 | (CT664) | (FHA domain) | |
| 0478 | (CT379) | hflX | GTP Binding Protein |
| 0703 | (CT673) | S/T Protein Kinase | |
| 0095 | (CT301) | S/T Protein Kinase | |
| 0397 | (CT259) | PP2C Phosphatase Family | |
| 0037 | (CT337) | ptsH | PTS Phosphocarrier Protein Hpr |
| 0038 | (CT336) | ptsI | PTS PEP Phosphotransferase |
| 0060 | (CT291) | ptsN_1 | PTS IIA Protein_1 |
| 0061 | (CT290) | ptsN_2 | PTS IIA Protein + HTH DNA-Binding Domain |
| 0262 | (CT218) | surE | SurE-like Acid Phosphatase |
| 0838 | (CT698) | thdF | Thiophene/Furan Oxidation Protein |
| 0693 | (CT683) | TFR Repeats-CT683 Hypothetical Protein | |
| 0321 | (CT092) | ychF | GTP Binding Protein |
| 0544 | (CT418) | yhbZ | GTP binding protein |
| 0844 | (CT703) | yphC | GTPase/GTP-binding protein |
| Standard Protein Secretion | |||
| 0115 | (CT025) | flh | Signal Recognition Particle GTPase |
| 0363 | (CT060) | flhA | Flagellar Secretion Protein |
| 0858 | (CT717) | fliI | Flagellum-specific ATP Synthase |
| 0704 | (CT672) | fliN | Flagellar Motor Switch Domain/YscQ family |
| 0815 | (CT572) | gspD | Gen. Secretion Protein D |
| 0816 | (CT571) | gspE | Gen. Secretion Protein E |
| 0817 | (CT570) | gspF | Gen. Secretion Protein F |
| 0359 | (CT064) | lepA | GTPase |
| 0110 | (CT020) | lepB | Signal Peptidase I |
| 0535 | (CT408) | lspA | Lipoprotein Signal Peptidase |
| 0260 | (CT141) | secA_1 | Protein Translocase Subunit_1 |
| 0841 | (CT701) | secA_2 | Translocase SecA_2 |
| 0564 | (CT448) | secD&secF | Protein Export Proteins SecD/SecF (fusion) |
| 0075 | (CT321) | secE | Preprotein Translocase |
| 0629 | (CT510) | secY | Translocase |
| 0848 | (CT707) | tig | Trigger Factor-Peptidyl-prolyl Isomerase |
| Transport-Related Proteins | |||
| 0486 | Hypothetical Proline Permease | ||
| 0289 | (CT230) | aaaT | Neutral Amino Acid (Glutamate) Transporter |
| 0691 | (CT685) | abcX | ABC Transporter ATPase |
| 1031 | (CT374) | arcD | Arginine/Ornithine Antiporter |
| 0482 | (CT381) | artJ | Arginine Periplasmic Binding Protein |
| 0836 | (CT554) | brnQ | Amino Acid (Branched) Transport |
| 0536 | (CT409) | dagA_1 | D-Ala/Gly Permease_1 |
| 0876 | (CT735) | dagA_2 | D-Alanine/Glycine Permease_2 |
| 0682 | (CT690) | dppD | ABC ATPase Dipeptide Transport |
| 0683 | (CT689) | dppF | ABC ATPase Dipeptide Transport |
| 0280 | (CT689) | dppF | Dipeptide Transporter ATPase |
| 0785 | (CT596) | exbB | Macromolecule Transporter |
| 0784 | (CT597) | exbD | Biopolymer Transport Protein |
| 0604 | (CT486) | fliY | Glutamine Binding Protein |
| 0192 | (CT129) | glnP | ABC Amino Acid Transporter Permease |
| 0191 | (CT130) | glnQ | ABC Amino Acid Transporter ATPase |
| 0528 | (CT401) | gltT | Glutamate Symport |
| 0286 | (CT194) | mgtE | Mg++ Transporter (CBS Domain) |
| 0413 | (CT264) | msbA | Transport ATP Binding Protein |
| 0290 | (CT231) | Na+-dependent Transporter | |
| 0195 | (CT198) | oppA_1 | Oligopeptide Binding Protein_1 |
| 0196 | (CT198) | oppA_2 | Oligopeptide Binding Protein_2 |
| 0197 | (CT139) | oppA_3 | Oligopeptide Binding Protein_3 |
| 0198 | (CT175) | oppA_4 | Oligopeptide Binding Protein_4 |
| 0599 | (CT480) | oppA_5 | Oligopeptide Binding Lipoprotein_5 |
| 0199 | (CT199) | oppB_1 | Oligopeptide Permease_1 |
| 0598 | (CT479) | oppB_2 | Oligopeptide Permease_2 |
| 0200 | (CT200) | oppC_1 | Oligopeptide Permease_1 |
| 0597 | (CT478) | oppC_2 | Oligopeptide Permease_2 |
| 0201 | (CT201) | oppD | Oligopeptide Transport ATPase |
| 0202 | (CT202) | oppF | Oligopeptide Transport ATPase |
| 0231 | (CT180) | tauB | ABC Transport ATPase (Nitrate/Fe) |
| 0782 | (CT599) | tolB | Macromolecule Transporter |
| 0969 | (CT817) | tyrP_1 | Tyrosine Transport_1 |
| 0970 | (CT818) | tyrP_2 | Tyrosine Transport_2 |
| 0665 | (CT544) | uhpC | Hexosphosphate Transport |
| 0282 | (CT216) | aasA | Amino Acid Transporter |
| 0207 | (CT204) | ybhI | dicarboxylate Translocator |
| 0971 | (CT819) | yccA | Transport Permease |
| 0248 | (CT152) | ycfV | ABC Transporter ATPase |
| 1014 | (CT856) | ychM | Sulfate Transporter |
| 0736 | (CT641) | ygeD | Efflux Protein |
| 0680 | (CT692) | ygo4 | Phosphate Permease |
| 0723 | (CT653) | yhbG | ABC Transporter ATPase |
| 0023 | (CT348) | yjjK | ABC Transporter Protein ATPase |
| 0127 | (CT034) | ytlF | Cationic Amino Acid Transporter |
| 0349 | (CT067) | ytgA | Solute Protein Binding Family |
| 0348 | (CT068) | ytgB | ABC Transporter ATPase |
| 0347 | (CT069) | ytgC | Integral Membrane Protein |
| 0346 | (CT070) | ytgD | Integral Membrane Protein |
| 1012 | (CT854) | yzcB | ABC Transporter Permease |
| 0868 | (CT727) | mtA | Metal Transport P-type ATPase |
| 0279 | Possible ABC Transporter Permease Protein | ||
| 0543 | (CT417) | (Metal Transport Protein) | |
| 0692 | (CT684) | ABC Transporter | |
| 0542 | (CT416) | ABC Transporter ATPase | |
| 0690 | (CT686) | ABC Transporter Membrane Protein | |
| 0541 | (CT415) | solute binding protein | |
| Type-III Secretion | |||
| 0323 | (CT090) | lcrD | Low Calcium Response D |
| 0324 | (CT089) | lcrE | Low Calcium Response E |
| 0811 | (CT576) | lcrH_1 | Low Ca Response Protein H_1 |
| 1021 | (CT862) | lcrH_2 | Low Calcium Response_2 |
| 0325 | (CT088) | sycE | Secretion Chaperone |
| 0702 | (CT674) | yscC | Yop C/Gen Secretion Protein D |
| 0828 | (CT559) | yscJ | Yop Translocation J |
| 0826 | (CT561) | yscL | Yop Translocation L |
| 0707 | (CT669) | yscN | Yop N (Flagellar-Type ATPase) |
| 0825 | (CT562) | yscR | Yop Translocation R |
| 0824 | (CT563) | yscS | YopS Translocation Protein |
| 0823 | (CT564) | yscT | YopT Translocation T |
| 0322 | (CT091) | ytcU | Yop Translocation Protein U |
| Central Intermediary Metabolism | |||
| Glycogen Metabolism | |||
| 0856 | (CT715) | UDP-Glucose Pyrophosphorylase | |
| 0948 | (CT798) | glgA | Glycogen Synthase |
| 0475 | (CT866) | glgB | Glucan Branching Enzyme |
| 0607 | (CT489) | glgC | Glucose-1-P Adenyltransferase |
| 0307 | (CT248) | glgP | Glycogen Phosphorylase |
| 0388 | (CT042) | glgX | Glycogen Hydrolase (debranching) |
| 0326 | (CT087) | malQ | Glucanotransferase |
| 0851 | (CT710) | pckA | Phosphoenolpyruvate Carboxykinase |
| Phosphorous & Sulfur | |||
| 0548 | (CT435) | cysI | Sulfite Reductase |
| 0920 | (CT774) | cysQ | Sulfite Synthesis/Biphosphate Phosphatase |
| 0025 | (CT346) | atsA | Sulphohydrolase |
| 0918 | (CT772) | ppa | Inorganic Pyrophosphatase |
| DNA Replication, Modification, Repair & Recombination | |||
| DNA Mismatch Repair | |||
| 0505 | 3-Methyladenine DNA Glycosylase | ||
| 0812 | (CT575) | mutL | DNA Mismatch Repair |
| 0941 | (CT792) | mutS | DNA Mismatch Repair |
| 0402 | (CT107) | mutY | Adenine Glycosylase |
| 0732 | (CT625) | nfo | Endonuclease IV |
| 0837 | (CT697) | nth | Endonuclease III |
| DNA Modification | |||
| 0596 | (CT477) | ada | Methyltransferase |
| 0114 | (CT024) | hemK | A/G-specific Methylase |
| 0891 | (CT748) | mfd | Transcription-Repair Coupling |
| 0620 | (CT501) | ruvA | Holliday Junction Helicase |
| 0390 | (CT040) | ruvB | Holliday Junction Helicase |
| 0621 | (CT502) | ruvC | Crossover Junction Endonuclease |
| 0053 | (CT298) | sms | Sms Protein |
| 0773 | (CT607) | ung | Uracil DNA Glycosylase |
| 1062 | (CT329) | xscA | Exodosyribonuclease VII |
| DNA Recombination | |||
| 0762 | (CT650) | recA | RecA Recombination Protein |
| 0738 | (CT639) | recB | Exodeoxyribonuclease V, Beta |
| 0737 | (CT640) | recC | Exodeoxyribonuclease V, Gamma |
| 0123 | (CT033) | recD_1 | Exodeoxyribonuclease V (Alpha Subunit)_1 |
| 0752 | (CT652) | recD_2 | Exodeoxyribonuclease V, Alpha_2 |
| 0339 | (CT074) | recF | ABC Superfamily ATPase |
| 0340 | (CT074) | (frame-shift with 0339) | |
| 0563 | (CT447) | recJ | ssDNA Exonuclease |
| 0299 | (CT240) | recR | Recombination Protein |
| DNA Replication | |||
| 0309 | (CT250) | dnaA_1 | Replication Initiation Protein_1 |
| 0424 | (CT275) | dnaA_2 | Replication Initiation Factor_2 |
| 0616 | (CT497) | dnaB | Replicative DNA Helicase |
| 0666 | (CT545) | dnaE | DNA Pol III Alpha |
| 0942 | (CT794) | dnaG | DNA Primase |
| 0338 | (CT075) | dnaN | DNA Pol III (Beta) |
| 0410 | (CT261) | dnaQ_1 | DNA Pol III Epsilon Chain_1 |
| 0655 | (CT536) | dnaQ_2 | DNA Pol III Epsilon Chain_2 |
| 0040 | (CT334) | dnaX_1 | DNA Pol III Gamma and Tau_1 |
| 0272 | (CT187) | dnaX_2 | DNA Pol III Gamma and Tau_2 |
| 0149 | (CT146) | dnU | DNA Ligase |
| 0274 | (CT189) | gyrA_1 | DNA Gyrase Subunit A_1 |
| 0716 | (CT660) | gyrA_2 | DNA Gyrase Subunit A_2 |
| 0275 | (CT190) | gyrB_1 | DNA Gyrase Subunit B_1 |
| 0715 | (CT661) | gyrB_2 | DNA Gyrase Subunit B_2 |
| 0416 | (CT267) | himD | Integration Host Factor Alpha |
| 0612 | (CT493) | polA | DNA Polymerase I |
| 0924 | (CT778) | priA | Primosomal Protein N |
| 0386 | (CT044) | ssb | SS DNA Binding Protein |
| 0835 | (CT555) | SWI/SNF family helicase_1 | |
| 0849 | (CT708) | SWI/SNF family helicase_2 | |
| 0769 | (CT643) | topA | DNA Topoisomerase I-Fused to SWI Domain |
| 0024 | (CT347) | xerC | Integrase/recombinase |
| 1024 | (CT864) | xerD | Integrase/recombinase |
| Eukaryotic-Type Chromatin Factors | |||
| 0886 | (CT743) | hctA | Histone-Like Developmental Protein |
| 0384 | (CT046) | hctB | Histone-like Protein 2 |
| 0878 | (CT737) | SET Domain protein | |
| 0577 | (CT460) | SWIB (YM74) Complex Protein | |
| UVR Exinuclease Repair System | |||
| 0096 | (CT333) | uvrA | Excinuclease ABC Subunit A |
| 0801 | (CT556) | uvrB | Excinuclease ABC Subunit B |
| 0940 | (CT791) | uvrC | Excinuclease ABC Subunit C |
| 0772 | (CT608) | uvrD | DNA Helicase |
| Energy Metabolism | |||
| Aerobic | |||
| 0855 | (CT714) | gpdA | Glycerol-3-P Dehydrogenase |
| 0743 | (CT634) | nqrA | Ubiquinone Oxidoreductase, Alpha |
| 0427 | (CT278) | nqr2 | NADH (Ubiquinone) Dehydrogenase |
| 0428 | (CT279) | nqr3 | NADH (Ubiquinone) Oxidoreductase, Gamma |
| 0429 | (CT280) | nqr4 | NADH (Ubiquinone) Reductase 4 |
| 0430 | (CT281) | nqr5 | NADH (Ubiquinone) Reductase 5 |
| 0883 | (CT740) | nqr6 | Phenolhydrolase/NADH (Ubiquinone) Oxidoreductase 6 |
| ATP Biogenesis and metabolism | |||
| 0351 | (CT065) | adt_1 | ADP/ATP Translocase_1 |
| 0614 | (CT495) | adt_2 | ADP/ATP Translocase_2 |
| 0088 | (CT308) | atpA | ATP Synthase Subunit A |
| 0089 | (CT307) | atpB | ATP Synthase Subunit B |
| 0090 | (CT306) | atpD | ATP Synthase Subunit D |
| 0086 | (CT310) | atpE | ATP Synthase Subunit E |
| 0091 | (CT305) | atpI | ATP Synthase Subunit I |
| 0092 | (CT304) | atpK | ATP Synthase Subunit K |
| 0860 | (CT719) | 0iF | Flagellar M-Ring Protein |
| Electron Transport Chain | |||
| 0102 | (CT013) | cydA | Cytochrome Oxidase Subunit I |
| 0103 | (CT014) | cydB | Cytochrome Oxidase Subunit II |
| 0364 | (CT059) | Ferredoxin | |
| 0084 | (CT312) | Predicted Ferredoxin | |
| Glycolysis & Gluconeogenesis | |||
| 0281 | (CT215) | dhnA | Predicted 1,6-Fructose Biphosphate Aldolase |
| 0800 | (CT587) | eno | Enolase |
| 0624 | (CT505) | gapA | Glyceraldehyde-3-P Dehydrogenase |
| 0056 | (CT295) | mrsA | Phosphomannomutase |
| 0967 | (CT815) | pgm | Phosphoglucomutase |
| 0160 | (CT207) | pfkA_1 | Fructose-6-P Phosphotransferase_1 |
| 0208 | (CT205) | pfkA_2 | Fructose-6-P Phosphotransferase_2 |
| 1025 | (CT378) | pgi | Glucose-6-P Isomerase |
| 0679 | (CT693) | pgk | Phosphoglycerate Kinase |
| 0863 | (CT722) | pgmA | Phosphoglycerate Mutase |
| 0097 | (CT332) | pyk | Pyruvate Kinase |
| 1063 | (CT328) | tpiS | Triosephosphate Isomerase |
| Pentose Phosphate Pathway | |||
| 0239 | (CT186) | devB | Glucose-6-P Dehydrogenase (DevB family) |
| 1060 | (CT331) | dxs | Transketolase |
| 0360 | (CT063) | gnd | 6-Phosphogluconate Dehydrogenase |
| 0185 | (CT121) | rpe | Ribulose-P Epimerase |
| 0141 | (CT213) | rpiA | Ribose-5-P Isomerase A |
| 0083 | (CT313) | tal | Transaldolase |
| 0893 | (CT750) | tktB | Transketolase |
| 0238 | (CT185) | zwf | Glucose-6-P Dehydrogenase |
| Pyruvate Dehydrogenase | |||
| 0833 | (CT557) | lpdA | Lipoamide Dehydrogenase |
| 0436 | (CT285) | lplA_1 | Lipoate Protein Ligase-Like Protein |
| 0618 | (CT499) | lplA_2 | Lipoate-Protein Ligase A |
| 0033 | (CT340) | pdhA&B | Oxoisovalerate Dehydrogenase α/β Fusion |
| 0304 | (CT245) | pdhA | Pyruvate Dehydrogenase Alpha |
| 0305 | (CT246) | pdhB | Pyruvate Dehydrogenase Beta |
| 0306 | (CT247) | pdhC | Dihydrolipoamide Acetyltransferase |
| TCA Cycle | |||
| 0495 | (CT390) | aspC | Aspartate Aminotransferase |
| 1013 | (CT855) | fumC | Fumarate Hydratase |
| 1028 | (CT376) | mdhC | Malate Dehydrogenase |
| 0789 | (CT592) | sdhA | Succinate Dehydrogenase |
| 0790 | (CT591) | sdhB | Succinate Dehydrogenase |
| 0788 | (CT593) | sdhC | Succinate Dehydrogenase |
| 0378 | (CT054) | sucA | Oxoglutarate Dehydrogenase |
| 0377 | (CT055) | sucB_1 | Dihydrolipoamide Succinyltransferase_1 |
| 0527 | (CT400) | sucB_2 | Dihydrolipoamide Succinyltransferase_2 |
| 0973 | (CT821) | sucC | Succinyl-CoA Synthetase, Beta |
| 0974 | (CT822) | sucD | Succinyl-CoA Synthetase, Alpha |
| Protein Folding, Assembly & Modification | |||
| Chaperones | |||
| 0949 | (CT799) | ctc | General Stress Protein |
| 0534 | (CT407) | dksA | DnaK Suppressor |
| 0032 | (CT341) | dnaJ | Heat Shock Protein J |
| 0503 | (CT396) | dnaK | Hsp-70 |
| 0134 | (CT110) | groEL_1 | Hsp-60_1 |
| 0777 | (CT604) | groEL_2 | Hsp-60_2 |
| 0898 | (CT755) | groEL_3 | Hsp-60_3 |
| 0135 | (CT111) | groES | 10 KDa Chaperonia |
| 0502 | (CT395) | grpE | HSP-70 Cofactor |
| 0661 | (CT541) | mip | FKBP-type Peptidyl-prolyl Cis-Trans Isomerase |
| Proteases | |||
| 0144 | (CT113) | clpB | Clp Protease ATPase |
| 0437 | (CT286) | clpC | ClpC Protease |
| 0520 | (CT431) | clpP_1 | CLP Protease |
| 0847 | (CT706) | clpP_2 | CLP Protease Subunit |
| 0846 | (CT705) | clpX | CLP Protease ATPase |
| 0269 | (CT138) | Dipeptidase | |
| 0998 | (CT841) | ftsH | ATP-dependent Zinc Protease |
| 0030 | (CT343) | gcp_1 | O-Sialoglycoprotein Endopeptidase_1 |
| 0194 | (CT197) | gcp_2 | O-Sialoglycoprotein Endopeptidase_2 |
| 0979 | (CT823) | htrA | DO Serine Protease |
| 0957 | (CT806) | ide | Insulinase family/Protease III |
| 0027 | (CT344) | lon | Lon ATP-dependent Protease |
| 1017 | (CT859) | lytB | Metalloprotease |
| 1009 | (CT851) | map | Methionine Aminopeptidase |
| 0385 | (CT045) | pepA | Leucyl Aminopeptidase A |
| 0136 | (CT112) | pepF | Oligopeptidase |
| 0813 | (CT574) | pepP | Aminopeptidase P |
| 0613 | (CT494) | sohB | Protease |
| 0555 | (CT441) | tsp | Tail-Specific Protease |
| 0344 | (CT072) | yaeL | Metalloprotease |
| 0981 | (CT824) | Zinc Metalloprotease (insulinase family) | |
| Protein Isomerases | |||
| 0227 | (CT176) | dsbB | Disulfide bond Oxidoreductase |
| 0786 | (CT595) | dsbD | Thio:disulfide Interchange Protein |
| 0228 | (CT177) | dsbG | Disulfide Bond Chaperone |
| 0933 | (CT783) | Predicted Disulfide Bond Isomerase | |
| 0926 | (CT780) | Thioredoxin Disulfide Isomerase | |
| Transcription | |||
| RNA Degradation | |||
| 0999 | (CT842) | pnp | Polyribonucleotide Nucleotidyltransferase |
| 0054 | (CT297) | mc | Ribonuclease III |
| 0119 | (CT029) | mhB_1 | Ribonuclease HII_1 |
| 1068 | (CT008) | mhB_2 | Ribonuclease HII_2 |
| 0934 | (CT784) | mpA | Ribonuclease P Protein Component |
| 0504 | (CT397) | vacB | Ribonuclease Family |
| RNA Elongation & Termination Factors | |||
| 0741 | (CT636) | greA | Transcription Elongation Factor |
| 0316 | (CT097) | nusA | N Utilization Protein A |
| 0076 | (CT320) | nusG | Transcriptional Antitermination |
| 0845 | (CT704) | pcnB_1 | Poly A Polymerase_1 |
| 0966 | (CT410) | pcnB_2 | Poly A Polymerase_2 |
| 0610 | (CT491) | rho | Transcription Termination Factor |
| RNA Methylases | |||
| 0674 | (CT553) | fmu | RNA Methyltransferase |
| 1059 | (CT354) | kgsA | Dimethyladenosine Transferase |
| 0187 | (CT133) | Predicted Methylase | |
| 0530 | (CT403) | spoU_1 | rRNA Methylase_1 |
| 0660 | (CT540) | spoU_2 | rRNA Methylase_2 |
| 0117 | (CT027) | trmD | tRNA (Guanine N-1)-Methyltransferase |
| 0885 | (CT742) | ygcA | rRNA Methyltransferase |
| 0986 | (CT829) | yggH | Predicted rRNA Methylase |
| 0987 | (CT830) | ytgB | Predicted rRNA Methylase |
| RNA Modification | |||
| 0649 | (CT530) | fmt | Methionyl tRNA Formyltransferase |
| 0910 | (CT766) | mizA | tRNA Pyrophosphate Transferase |
| 0719 | (CT658) | sfhB | Predicted Pseudouridine Synthase |
| 0219 | (CT193) | tgt | Queuine tRNA Ribosyl Transferase |
| 0580 | (CT463) | truA | Pseudouridylate Synthase I |
| 0319 | (CT094) | truB | tRNA Pseudouridine Synthase |
| 0403 | (CT106) | yceC | Predicted Pseudouridine Synthetase Family |
| 0864 | (CT723) | yjbC | Predicted Pseudouridine Synthase |
| RNA Polymerase & Transcription Regulators | |||
| 0586 | (CT468) | atpC | Two-Component Regulator |
| 0362 | (CT061) | rpsD | Sigma-28/WhiG Family |
| 0501 | (CT394) | hrcA | HTH Transcriptional Repressor |
| 0793 | (CT588) | rbsU | Sigma Regulatory Family Protein-PP2C Phosphatase (RsbW Antagonist) |
| 0626 | (CT507) | rpoA | RNA Polymerase Alpha |
| 0081 | (CT315) | rpoB | RNA Polymerase Beta |
| 0082 | (CT314) | rpoC | RNA Polymerase Beta' |
| 0756 | (CT615) | rpoD | RNA Polymerase Sigma-66 |
| 0771 | (CT609) | rpoN | RNA Polymerase Sigma-54 |
| 0511 | (CT424) | rsbV_1 | Sigma Regulatory Factor_1 |
| 0909 | (CT765) | rsbV_2 | Sigma Factor Regulator_2 |
| 0670 | (CT549) | rsbW | Sigma Regulatory Factor Histidine Kinase |
| 0750 | (CT630) | tctD | HTH Transcriptional Regulatory Protein + Receiver Doman |
| 1069 | (CT009) | yfgA | HTH Transcriptional Regulator |
| Translation | |||
| Amino Acyl tRNA Synthesis | |||
| 0892 | (CT749) | alaS | Alanyl tRNA Synthetase |
| 0570 | (CT454) | argS | Arginyl tRNA Transferase |
| 0662 | (CT542) | aspS | Aspartyl tRNA Synthetase |
| 0932 | (CT782) | cysS | Cysteinyl tRNA Synthetase |
| 0003 | (CT003) | gatA | Glu tRNA Gln Amidotransferase (A subunit) |
| 0004 | (CT004) | gatB | Glu tRNA Gln Amidotransferase (B Subunit) |
| 0002 | (CT002) | gatC | Glu tRNA Gln Amidotransferase (C subunit) |
| 0560 | (CT445) | gltX | Glutamyl-tRNA Synthetase |
| 0946 | (CT796) | glyQ | Glycyl tRNA Synthetase |
| 0663 | (CT543) | hisS | Histidyl tRNA Synthetase |
| 0109 | (CT019) | ileS | Isoleucyl-tRNA Synthetase |
| 0153 | (CT209) | leuS | Leucyl tRNA Synthetase |
| 0931 | (CT781) | lysS | Lysyl tRNA Synthetase |
| 0122 | (CT032) | metG | Methionyl-tRNA Synthetase |
| 0993 | (CT836) | pheS | Phenylalanyl tRNA Synthetase, Alpha |
| 0594 | (CT475) | pheT | Phenylalanyl tRNA Synthetase Beta |
| 0500 | (CT393) | proS | Prolyl tRNA Synthetase |
| 0870 | (CT729) | serS | Seryl tRNA Synthetase_2 |
| 0806 | (CT581) | thrS | Threonyl tRNA Synthetase |
| 0802 | (CT585) | trpS | Tryptophanyl tRNA Synthetase |
| 0361 | (CT062) | tyrS | Tyrosyl tRNA Synthetase |
| 0094 | (CT302) | valS | Valyl tRNA Synthetase |
| Peptide Chain Initiation, Elongation & Termination | |||
| 1067 | (CT353) | def | Polypeptide Deformylase |
| 0184 | (CT122) | efp_1 | Elongation Factor P_1 |
| 0895 | (CT752) | efp_2 | Elongation Factor P_2 |
| 0550 | (CT437) | fusA | Elongation Factor G |
| 0073 | (CT323) | infA | Initiation Factor IF-1 |
| 0317 | (CT096) | infB | Initiation Factor-2 |
| 0990 | (CT833) | infC | Initiation Factor 3 |
| 0113 | (CT023) | pfrA | Peptide Chain Releasing Factor 1 |
| 0576 | (CT459) | prfB | Peptide Chain Release Factor 2 |
| 0950 | (CT800) | pth | Peptidyl tRNA Hydrolase |
| 0318 | (CT095) | rbfA | Ribosome Binding Factor A |
| 0699 | (CT677) | rrf | Ribosome Releasing Factor |
| 0697 | (CT679) | tsf | Elongation Factor TS |
| 0074 | (CT322) | tufA | Elongation Factor Tu |
| Ribosomal Proteins | |||
| 0078 | (CT318) | rl1 | L1 Ribosomal Protein |
| 0644 | (CT525) | rl2 | L2 Ribosomal Protein |
| 0647 | (CT528) | rl3 | L3 Ribosomal Protein |
| 0646 | (CT527) | rl4 | L4 Ribosomal Protein |
| 0635 | (CT516) | rl5 | L5 Ribosomal Protein |
| 0633 | (CT514) | rl6 | L6 Ribosomal Protein |
| 0080 | (CT316) | rl7 | L7/L12 Ribosomal Protein |
| 0953 | (CT803) | rl9 | L9 Ribosomal Protein |
| 0079 | (CT317) | rl10 | L10 Ribosomal Protein |
| 0077 | (CT319) | rl11 | L11 Ribosomal Protein |
| 0247 | (CT125) | rl13 | L13 Ribosomal Protein |
| 0637 | (CT518) | rl14 | L14 Ribosomal Protein |
| 0630 | (CT511) | rl15 | L15 Ribosomal Protein |
| 0640 | (CT521) | rl16 | L16 Ribosomal Protein |
| 0625 | (CT506) | rl17 | L17 Ribosomal Protein |
| 0632 | (CT513) | rl18 | L18 Ribosomal Protein |
| 0118 | (CT028) | rl19 | L19 Ribosomal Protein |
| 0992 | (CT835) | rl20 | L20 Ribosomal Protein |
| 0546 | (CT420) | rl21 | L21 Ribosomal Protein |
| 0642 | (CT523) | rl22 | L22 Ribosomal Protein |
| 0645 | (CT526) | rl23 | L23 Ribosomal Protein |
| 0636 | (CT517) | rl24 | L24 Ribosomal Protein |
| 0545 | (CT419) | rl27 | L27 ribosomal protein |
| 0327 | (CT086) | rl28 | L28 Ribosomal Protein |
| 0639 | (CT520) | rl29 | L29 Ribosomal Protein |
| 0112 | (CT022) | rl31 | L31 Ribosomal Protein |
| 0961 | (CT810) | rl32 | L32 Ribosomal Protein |
| 0250 | (CT150) | rl33 | L33 Ribosomal Protein |
| 0935 | (CT785) | rl34 | L34 Ribosomal Protein |
| 0991 | (CT834) | rl35 | L35 Ribosomal Protein |
| 0936 | (CT786) | rl36 | L36 Ribosomal Protein |
| 0315 | (CT098) | rs1 | S1 Ribosomal Protein |
| 0696 | (CT680) | rs2 | S2 Ribosomal Protein |
| 0641 | (CT522) | rs3 | S3 Ribosomal Protein |
| 0733 | (CT626) | rs4 | S4 Ribosomal Protein |
| 0631 | (CT512) | rs5 | S5 Ribosomal Protein |
| 0951 | (CT801) | rs6 | S6 Ribosomal Protein |
| 0551 | (CT438) | rs7 | S7 Ribosomal Protein |
| 0634 | (CT515) | rs8 | S8 Ribosomal Protein |
| 0246 | (CT126) | rs9 | S9 Ribosomal Protein |
| 0549 | (CT436) | rs10 | S10 Ribosomal Protein |
| 0627 | (CT508) | rs11 | S11 Ribosomal Protein |
| 0552 | (CT439) | rs12 | S12 Ribosomal Protein |
| 0628 | (CT509) | rs13 | S13 Ribosomal Protein |
| 0937 | (CT787) | rs14 | S14 Ribosomal Protein |
| 1000 | (CT843) | rs15 | S15 Ribosomal Protein |
| 0116 | (CT026) | rs16 | S16 Ribosomal Protein |
| 0638 | (CT519) | rs17 | S17 Ribosomal Protein |
| 0952 | (CT802) | rs18 | S18 Ribosomal Protein |
| 0643 | (CT524) | rs19 | S19 Ribosomal Protein |
| 0754 | (CT617) | rs20 | S20 Ribosomal Protein |
| 0031 | (CT342) | rs21 | S21 Ribosomal Protein |
| Other Categories | |||
| Chlamydia-Specific Proteins | |||
| 0561 | (CT446) | Euo | CHLPS Euo Protein |
| 0804 | (CT583) | Gp6D | CHLTR Plasmid Paralog |
| 0186 | (CT119) | Similarity to IncA_1 | |
| 0291 | (CT232) | incB | Inclusion Membrane Protein B |
| 0292 | (CT233) | incC | Inclusion Membrane Protein C |
| 1026 | (CT377) | LtuA Protein | |
| 0333 | (CT080) | LtuB Protein | |
| 0005 | (CT871) | pmp_1 | Polymorphic Outer Membrane Protein G Family |
| 0013 | (CT871) | pmp_2 | Polymorphic Outer Membrane Protein G Family |
| 0014 | (CT871) | pmp_3 | Polymorphic Outer Membrane Protein G Family |
| 0015 | (CT871) | pmp_3 | PMP_3 (frame-shift with 0014) |
| 0016 | (CT874) | pmp_4 | Polymorphic Outer Membrane Protein G Family |
| 0017 | (CT871) | pmp_4 | PMP_4 (frame-shift with 0016) |
| 0018 | (CT874) | pmp_5 | Polymorphic Outer Membrane Protein G Family |
| 0019 | (CT871) | pmp_5 | PMP_5 (frame-shift with 0018) |
| 0444 | (CT871) | pmp_6 | Polymorphic Outer Membrane Protein G/I Family |
| 0445 | (CT871) | pmp_7 | Polymorphic Outer Membrane Protein G Family |
| 0446 | (CT871) | pmp_8 | Polymorphic Outer Membrane Protein G Family |
| 0447 | (CT871) | pmp_9 | Polymorphic Outer Membrane Protein G/I Family |
| 0450 | (CT871) | pmp_10 | Polymorphic Outer Membrane Protein G Family |
| 0449 | (CT871) | pmp_10 | PMP_10 (Frame-shift with 0450) |
| 0451 | (CT871) | pmp_11 | Polymorphic Outer Membrane Protein G Family |
| 0452 | (CT874) | pmp_12 | Polymorphic Outer Membrane Protein (truncated) A/I Family |
| 0453 | (CT871) | pmp_13 | Polymorphic Outer Membrane Protein G Family |
| 0454 | (CT872) | pmp_14 | Polymorphic Outer Membrane Protein H Family |
| 0466 | (CT869) | pmp_15 | Polymorphic Outer Membrane Protein E Family |
| 0467 | (CT869) | pmp_16 | Polymorphic Outer Membrane Protein E Family |
| 0468 | (CT869) | pmp_17 | Polymorphic Outer Membrane Protein E Family |
| 0469 | (CT869) | pmp_17 | PMP_17 (Frame-shift with 0468) |
| 0470 | (CT869) | pmp_17 | PMP_17 (Frame-shift with 0469) |
| 0471 | (CT870) | pmp_18 | Polymorphic Outer Membrane Protein E/F Family |
| 0539 | (CT412) | pmp_19 | Polymorphic Membrane Protein A Family |
| 0540 | (CT413) | pmp_20 | Polymorphic Membrane Protein B Family |
| 0963 | (CT812) | pmp_21 | Polymorphic Membrane Protein D Family |
| 0562 | CHLPS 43 kDa Protein Homolog_1 | ||
| 0927 | CHLPS 43 kDa Protein Homolog_2 | ||
| 0928 | CHLPS 43 kDa Protein Homolog_3 | ||
| 0929 | CHLPS 43 kDa Protein Homolog_4 | ||
| 0728 | (CT622) | CHLPN 76 kDa Homolog_1 (CT622) | |
| 0729 | (CT623) | CHLPN 76 kDa Homolog_2 (CT623) | |
| 0133 | (CT109) | CHLPS Hypothetical Protein | |
| 0332 | (CT081) | CHLPR T2 Protein | |
| Miscellaneous Enzymes/Conserved Proteins | |||
| 0193 | argR | Possible Arginine Repressor | |
| 1046 | Aromatic Amino Acid Hydroxylase | ||
| 0232 | Similarity to 5'-Methylthioadenosine Nucleosidase | ||
| 0128 | (CT035) | Biotin Protein Ligase | |
| 0513 | (CT426) | Fe--S Oxidoreductase_1 | |
| 0911 | (CT767) | Fe--S Oxidoreductase_2 | |
| 0373 | (CT057) | gcpE | GcpE Protein |
| 0407 | (CT103) | HAD Superfamily Hydrolase/Phosphatase | |
| 0917 | (CT771) | Hydrolase/Phosphatase Homolog | |
| 0488 | (CT385) | ycfF | HIT Family Hydrolase |
| 0701 | (CT675) | karG | Arginine Kinase |
| 0526 | (CT399) | kpsF | GurQ/KpsF Family Sugar-P Isomerase |
| 0919 | (CT773) | ldh | Leucine Dehydrogenase |
| 0022 | (CT349) | maf | Maf protein |
| 0997 | (CT840) | mesJ | PP-loop superfamily ATPase |
| 0151 | (CT148) | mhpA | Monooxygenase |
| 0730 | (CT624) | mviN | Integral Membrane Protein |
| 0861 | (CT720) | NifU-Related Protein | |
| 0479 | (CT380) | phnP | Metal Dependent Hydrolase |
| 0106 | (CT015) | phoH | ATPase |
| 0329 | (CT084) | Phospholipase D Superfamily | |
| 0435 | (CT284) | Phospholipase D Superfamily | |
| 0581 | (CT464) | Phosphoglycolate Phosphatase | |
| 0897 | (CT754) | Predicted Phosphohydrolase | |
| 0509 | (CT422) | Predicted Metalloenzyme | |
| 1030 | (CT375) | Predicted D-Amino Acid Dehydrogenase | |
| 0531 | (CT404) | SAM Dependent Methyltransferase | |
| 0337 | (CT076) | smpB | Small Protein B |
| 0394 | (CT256) | tlyC_1 | CBS Domain Protein (Hemolysin Homolog)_1 |
| 0510 | (CT423) | tlyC_2 | CBS Domains (Hemolysin Homolog)_2 |
| 0382 | (CT048) | yabC | SAM-Dependent Methyltransferase |
| 0787 | (CT594) | yabD | PHF Superfamily (Urease/Pyrimidinase) Hydrolase |
| 0611 | (CT492) | yacE | Predicted Phosphatase/Kinase |
| 0579 | (CT462) | yacM | Sugar Nucleotide Phosphorylase |
| 0578 | (CT461) | yaeI | Phosphohydrolase |
| 0345 | (CT071) | yaeM | CT071 Hypothetical Protein |
| 0566 | (CT450) | yaeS | YaeS family Hypothetical Protein |
| 0591 | (CT472) | yagE | YagE family |
| 0039 | (CT335) | ybaB | YbaB family Hypothetical Protein |
| 0101 | (CT012) | ybbP | YbbP family Hypothetical Protein |
| 0915 | (CT769) | ybeB | iojap Superfamily Onholog |
| 0137 | (CT108) | ybgI | ACR family |
| 0529 | (CT402) | ycaH | ATPase |
| 0438 | (CT287) | ycbF | PP-loop Superfamily ATPase |
| 0734 | (CT627) | yccA | YccA Hypothetical Protein |
| 0954 | (CT804) | ychB | Predicted Kinase |
| 0261 | (CT217) | ydaO | PP-Loop Superfamily ATPase |
| 0245 | (CT127) | ydhO | Polysaccharide Hydrolase-Invasin Repeat Family |
| 0573 | (CT457) | yebC | YebC Family Hypothetical Protein |
| 0689 | (CT687) | yfhO_1 | NifS-related Aminotransferase_1 |
| 0862 | (CT721) | yfhO_2 | NifS-related Aminotransferase_2 |
| 0547 | (CT434) | ygbB | YgbB Family Hypothetical Protein |
| 0237 | (CT184) | yggF | YggF Family Hypothetical Protein |
| 0775 | (CT606) | yggY | YggY Family Hypothetical Protein |
| 0396 | (CT258) | yhfO_3 | NifS-related Aminotransferase_3 |
| 0605 | (CT487) | yhhF | Predicted Methylase |
| 0575 | (CT458) | yhhY | Amino Group Acetyl Transferase |
| 0592 | (CT473) | yidD | YidD Family |
| 0982 | (CT825) | yigN | YigN Family Hypothetical Protein |
| 0657 | (CT537) | yjeE | YjeE Hypothetical Protein |
| 0768 | (CT644) | yohI | YohI Predicted Oxidoreductase |
| 0336 | (CT077) | yojL | YojL Hypothetical Protein |
| 0217 | (CT140) | ypdP | YpdP Hypothetical Protein |
| 0140 | (CT212) | yqdE | YqdE Hypothetical Protein |
| 0263 | (CT221) | yqfU | YqfU Hypothetical Protein |
| 0139 | (CT211) | yqgE | YqgE Hypothetical Protein |
| 0270 | (CT137) | ywlC | SuAS Superfamily-related Protein |
| 0879 | (CT738) | yycJ | Metal Dependent Hydrolase |
| Homologs to CHLTR Hypothetical Coding Genes | |||
| 0001 | (CT001) | CT001 Hypothetical Protein | |
| 0020 | (CT351) | CT351 Hypothetical Protein | |
| 0021 | (CT350) | CT350 Hypothetical Protein | |
| 0026 | (CT345) | CT345 Hypothetical Protein | |
| 0035 | (CT339) | CT339 Hypothetical Protein | |
| 0036 | (CT338) | CT338 Hypothetical Protein | |
| 0055 | (CT296) | CT296 Hypothetical Protein | |
| 0062 | (CT289) | CT289 Hypothetical Protein | |
| 0065 | (CT288) | CT288 Hypothetical Protein | |
| 0068 | (CT360) | CT360 Hypothetical Protein | |
| 0071 | (CT325) | CT325 Hypothetical Protein | |
| 0072 | (CT324) | CT324 Hypothetical Protein | |
| 0085 | (CT311) | CT311 Hypothetical Protein | |
| 0087 | (CT309) | CT309 Hypothetical Protein | |
| 0093 | (CT303) | CT303 Hypothetical Protein | |
| 0100 | (CT011) | CT011 Hypothetical Protein | |
| 0104 | (CT017) | CT017 Hypothetical Protein | |
| 0105 | (CT016) | CT016 Hypothetical Protein | |
| 0107 | (CT058) | CT058 Hypothetical Protein_1 | |
| 0108 | (CT018) | CT018 Similarity | |
| 0111 | (CT021) | CT021 Hypothetical Protein | |
| 0121 | (CT031) | CT031 Hypothetical Protein | |
| 0129 | (CT036) | CT036 Similarity | |
| 0145 | (CT114) | CT114 Hypothetical Protein | |
| 0150 | (CT147) | CT147 Hypothetical Protein | |
| 0152 | (CT149) | CT149 Hypothetical Protein | |
| 0176 | (CT153) | CT153 Hypothetical Protein | |
| 0188 | (CT132) | CT132 Hypothetical Protein | |
| 0189 | (CT131) | CT131 Hypothetical Protein | |
| 0206 | (CT203) | CT203 Hypothetical Protein | |
| 0229 | (CT178) | CT178 Hypothetical Protein | |
| 0230 | (CT179) | CT179 Hypothetical Protein | |
| 0234 | (CT181) | CT181 Hypothetical Protein | |
| 0249 | (CT151) | CT151 Hypothetical Protein | |
| 0253 | (CT144) | CT144 Hypothetical Protein_1 | |
| 0254 | (CT143) | CT143 Hypothetical Protein_1 | |
| 0255 | (CT142) | CT142 Hypothetical Protein_1 | |
| 0256 | (CT144) | CT144 Hypothetical Protein_2 | |
| 0257 | (CT143) | CT143 Hypothetical Protein_2 | |
| 0259 | (CT142) | CT142 Hypothetical Protein_2 | |
| 0276 | (CT191) | CT191 Hypothetical Protein | |
| 0288 | (CT195) | CT195 Hypothetical Protein | |
| 0293 | (CT234) | CT234 Hypothetical Protein | |
| 0301 | (CT242) | CT368 Hypothetical Protein | |
| 0303 | (CT244) | CT244 Hypothetical Protein | |
| 0308 | (CT249) | CT249 Similarity | |
| 0312 | (CT101) | CT101 Hypothetical Protein | |
| 0328 | (CT085) | CT085 Hypothetical Protein | |
| 0330 | (CT083) | CT083 Hypothetical Protein | |
| 0331 | (CT082) | CT082 Hypothetical Protein | |
| 0334 | (CT079) | CT079 Similarity | |
| 0342 | (CT073) | CT073 Hypothetical Protein | |
| 0343 | (CT073) | (frame-shift with 0342?) | |
| 0350 | (CT066) | CT066 Hypothetical Protein | |
| 0369 | (CT058) | CT058 Hypothetical Protein_2 | |
| 0370 | (CT058) | CT058 Hypothetical Protein_3 | |
| 0374 | (CT056) | CT056 Hypothetical Protein | |
| 0379 | (CT053) | CT053 Hypothetical Protein | |
| 0381 | (CT326) | CT326 Similarity | |
| 0383 | (CT047) | CT047 Hypothetical Protein | |
| 0387 | (CT043) | CT043 Hypothetical Protein | |
| 0389 | (CT041) | CT041 Hypothetical Protein | |
| 0393 | (CT038) | CT038 Hypothetical Protein | |
| 0395 | (CT257) | CT257 Hypothetical Protein | |
| 0399 | (CT253) | CT253 Hypothetical Protein | |
| 0400 | (CT254) | CT254 Hypothetical Protein | |
| 0401 | (CT255) | CT255 Hypothetical Protein | |
| 0405 | (CT105) | CT105 Hypothetical Protein | |
| 0408 | (CT102) | CT102 Hypothetical Protein | |
| 0409 | (CT260) | CT260 Hypothetical Protein | |
| 0411 | (CT262) | CT262 Hypothetical Protein | |
| 0412 | (CT263) | CT263 Hypothetical Protein | |
| 0415 | (CT266) | CT266 Hypothetical Protein | |
| 0420 | (CT271) | CT271 Hypothetical Protein | |
| 0422 | (CT273) | CT273 Hypothetical Protein | |
| 0423 | (CT274) | CT274 Hypothetical Protein | |
| 0425 | (CT276) | CT276 Hypothetical Proteins | |
| 0426 | (CT277) | CT277 Similarity | |
| 0434 | (CT283) | CT283 Hypothetical Protein | |
| 0441 | (CT007) | CT007 Hypothetical Protein | |
| 0442 | (CT006) | CT006 Hypothetical Protein | |
| 0443 | (CT005) | CT005 Hypothetical Protein | |
| 0474 | (CT365) | CT365 Hypothetical Protein | |
| 0476 | (CT865) | CT865 Hypothetical Protein | |
| 0480 | (CT383) | CT383 Hypothetical Protein | |
| 0485 | (CT382) | CT382.1 Hypothetical Protein | |
| 0487 | (CT384) | CT384 Hypothetical Protein | |
| 0489 | (CT386) | CT386 Hypothetical Protein | |
| 0490 | (CT387) | CT387 Hypothetical Protein | |
| 0491 | (CT389) | CT389 Hypothetical Protein | |
| 0496 | (CT391) | CT391 Hypothetical Protein | |
| 0497 | (CT388) | CT388 Hypothetical Protein | |
| 0506 | (CT421) | CT421 Hypothetical Protein | |
| 0507 | (CT421) | CT421.1 Hypothetical Protein | |
| 0508 | (CT421) | CT421.2 Hypothetical Protein | |
| 0512 | (CT425) | CT425 Hypothetical Protein | |
| 0514 | (CT427) | CT427 Hypothetical Protein | |
| 0518 | (CT429) | CT429 Hypothetical Protein | |
| 0522 | (CT433) | CT433 Hypothetical Protein | |
| 0525 | (CT398) | CT398 Hypothetical Protein | |
| 0533 | (CT406) | CT406 Hypothetical Protein | |
| 0537 | (CT814) | CT814.1 Hypothetical Protein | |
| 0538 | (CT814) | CT814 Hypothetical Protein | |
| 0554 | (CT440) | CT440 Hypothetical Protein | |
| 0559 | (CT441) | CT441.1 Hypothetical Protein | |
| 0565 | (CT449) | CT449 Hypothetical Protein | |
| 0572 | (CT456) | CT456 Hypothetical Protein | |
| 0582 | (CT465) | CT465 Hypothetical Protein | |
| 0583 | (CT466) | CT466 Hypothetical Protein | |
| 0588 | (CT469) | CT469 Hypothetical Protein | |
| 0589 | (CT470) | CT470 Hypothetical Protein | |
| 0590 | (CT471) | CT471 Hypothetical Protein | |
| 0593 | (CT474) | CT474 Hypothetical Protein | |
| 0595 | (CT476) | CT476 Hypothetical Protein | |
| 0601 | (CT483) | CT483 Hypothetical Protein | |
| 0602 | (CT484) | CT484 Hypothetical Protein | |
| 0606 | (CT488) | CT488 Hypothetical Protein | |
| 0609 | (CT490) | CT490 Hypothetical Protein | |
| 0622 | (CT503) | CT503 Hypothetical Protein | |
| 0623 | (CT504) | CT504 Hypothetical Protein | |
| 0648 | (CT529) | CT529 Hypothetical Protein | |
| 0658 | (CT538) | CT538 Hypothetical Protein | |
| 0667 | (CT546) | CT546 Hypothetical Protein | |
| 0668 | (CT547) | CT547 Hypothetical Protein | |
| 0669 | (CT548) | CT548 Hypothetical Protein | |
| 0671 | (CT550) | CT550 Hypothetical Protein | |
| 0673 | (CT552) | CT552 Hypothetical Protein | |
| 0675 | (CT696) | CT696 Hypothetical Protein | |
| 0676 | (CT695) | CT695 Similarity | |
| 0681 | (CT691) | CT691 Hypothetical Protein | |
| 0687 | (CT482) | CT482 Hypothetical Protein | |
| 0688 | (CT481) | CT481 Hypothetical Protein | |
| 0700 | (CT676) | CT676 Hypothetical Protein | |
| 0705 | (CT671) | CT671 Hypothetical Protein | |
| 0706 | (CT670) | CT670 Hypothetical Protein | |
| 0708 | (CT668) | CT668 Hypothetical Protein | |
| 0709 | (CT667) | CT667 Hypothetical Protein | |
| 0710 | (CT666) | CT666 Hypothetical Protein | |
| 0711 | (CT665) | CT665 Hypothetical Protein | |
| 0713 | (CT663) | CT663 Hypothetical Protein | |
| 0717 | (CT656) | CT656 Hypothetical Protein | |
| 0718 | (CT657) | CT657 Hypothetical Protein | |
| 0720 | (CT659) | CT659 Hypothetical Protein | |
| 0722 | (CT654) | CT654 Hypothetical Protein | |
| 0725 | (CT652) | CT652.1 Hypothetical Protein | |
| 0726 | (CT620) | CT620 Hypothetical Protein | |
| 0727 | (CT619) | CT619 Hypothetical Protein | |
| 0739 | (CT638) | CT368 Hypothetical Protein | |
| 0742 | (CT635) | CT635 Hypothetical Protein | |
| 0746 | (CT632) | CT632 Hypothetical Protein | |
| 0747 | (CT631) | CT631 Hypothetical Protein | |
| 0751 | (CT651) | CT651 Hypothetical Protein | |
| 0755 | (CT616) | CT616 Hypothetical Protein | |
| 0760 | (CT611) | CT611 Hypothetical Protein | |
| 0761 | (CT610) | CT610 Hypothetical Protein | |
| 0764 | (CT648) | CT648 Hypothetical Protein | |
| 0765 | (CT647) | CT647 Hypothetical Protein | |
| 0766 | (CT646) | CT646 Hypothetical Protein | |
| 0767 | (CT645) | CT645 Hypothetical Protein | |
| 0770 | (CT642) | CT642 Hypothetical Protein | |
| 0774 | (CT606) | CT606.1 Hypothetical Protein | |
| 0776 | (CT605) | CT605 Hypothetical Protein | |
| 0779 | (CT602) | CT602 Hypothetical Protein | |
| 0783 | (CT598) | CT598 Hypothetical Protein | |
| 0791 | (CT590) | CT590 Hypothetical Protein | |
| 0792 | (CT589) | CT589 Hypothetical Protein | |
| 0803 | (CT584) | CT584 Hypothetical Protein | |
| 0807 | (CT580) | CT580 Hypothetical Protein | |
| 0808 | (CT579) | CT579 Hypothetical Protein | |
| 0809 | (CT578) | CT578 Hypothetical Protein | |
| 0810 | (CT577) | CT577 Hypothetical Protein | |
| 0814 | (CT573) | CT573 Hypothetical Protein | |
| 0818 | (CT569) | CT569 Hypothetical Protein | |
| 0819 | (CT568) | CT568 Hypothetical Protein | |
| 0820 | (CT567) | CT567 Hypothetical Protein | |
| 0821 | (CT566) | CT566 Hypothetical Protein | |
| 0822 | (CT565) | CT565 Hypothetical Protein | |
| 0827 | (CT560) | CT560 Hypothetical Protein | |
| 0834 | (CT556) | CT556 Hypothetical Protein | |
| 0840 | (CT700) | CT700 Hypothetical Protein | |
| 0842 | (CT702) | CT702 Hypothetical Protein | |
| 0843 | (CT702) | CT702 Hypothetical Protein | |
| 0852 | (CT711) | CT711 Hypothetical Protein | |
| 0853 | (CT712) | CT712 Hypothetical Protein | |
| 0857 | (CT716) | CT716 Hypothetical Protein | |
| 0859 | (CT718) | CT718 Hypothetical Protein | |
| 0865 | (CT724) | CT724 Hypothetical Protein | |
| 0869 | (CT728) | CT728 Hypothetical Protein | |
| 0874 | (CT733) | CT733 Hypothetical Protein | |
| 0875 | (CT734) | CT734 Hypothetical Protein | |
| 0884 | (CT741) | CT741 Hypothetical Protein | |
| 0887 | (CT744) | CHLTR Possible Phosphoprotein | |
| 0896 | (CT753) | CT753 Hypothetical Protein | |
| 0906 | (CT763) | CT763 Hypothetical Protein | |
| 0908 | (CT764) | CT764 Hypothetical Protein | |
| 0912 | (CT768) | CT768 Hypothetical Protein | |
| 0925 | (CT779) | CT779 Hypothetical Protein | |
| 0938 | (CT788) | CT788 Hypothetical Protein | |
| 0939 | (CT790) | CT790 Hypothetical Protein | |
| 0943 | (CT794) | CT794.1 Hypothetical Protein | |
| 0945 | (CT795) | CT795 Hypothetical Protein | |
| 0956 | (CT805) | CT805 Hypothetical Protein | |
| 0960 | (CT809) | CT809 Hypothetical Protein | |
| 0989 | (CT832) | CT832 Hypothetical Protein | |
| 0994 | (CT837) | CT837 Hypothetical Protein | |
| 0995 | (CT838) | CT838 Hypothetical Protein | |
| 0996 | (CT839) | CT839 Hypothetical Protein | |
| 1002 | (CT845) | CT845 Hypothetical Protein | |
| 1003 | (CT846) | CT846 Hypothetical Protein | |
| 1004 | (CT847) | CT847 Hypothetical Protein | |
| 1005 | (CT848) | CT848 Hypothetical Protein | |
| 1006 | (CT849) | CT849 Hypothetical Protein | |
| 1007 | (CT849) | CT849.1 Hypothetical Protein | |
| 1008 | (CT850) | CT850 Hypothetical Protein | |
| 1010 | (CT852) | CT852 Hypothetical Protein | |
| 1011 | (CT853) | CT853 Hypothetical Protein | |
| 1015 | (CT857) | CT857 Hypothetical Protein | |
| 1016 | (CT858) | CT858 Hypothetical Protein | |
| 1019 | (CT860) | CT860 Hypothetical Protein | |
| 1020 | (CT861) | CT861 Hypothetical Protein | |
| 1022 | (CT863) | CT863 Hypothetical Protein | |
| 1032 | (CT373) | CT373 Hypothetical Protein | |
| 1033 | (CT372) | CT372 Hypothetical Protein | |
| 1034 | (CT371) | CT371 Hypothetical Protein | |
| 1057 | (CT356) | CT356 Hypothetical Protein | |
| 1058 | (CT355) | CT355 Hypothetical Protein | |
| 1061 | (CT330) | CT330 Hypothetical Protein | |
| 1073 | (CT371) | CT371 Hypothetical Protein | |
| Coding Genes Not in C. trachamatis | |||
| 0486 | Hypothetical Proline Permease | ||
| 0279 | Possible ABC Transporter Permease Protein | ||
| 0505 | 3-Methyladenine DNA Glycosylase | ||
| 0193 | argR | Similarity to Arginine Repressor | |
| 1041 | bioA | Adenosylmethionine-8-Amino-7-Oxononanoate Aminotransferase | |
| 1044 | bioB | Biotin Synthase | |
| 1042 | bioD | Dethiobiotin synthetase | |
| 0585 | Similarity to Cps IncA_2 | ||
| 0562 | CHLPS 43 kDa Protein Homolog_1 | ||
| 0927 | CHLPS 43 kDa Protein Homolog_2 | ||
| 0928 | CHLPS 43 kDa Protein Homolog_3 | ||
| 0929 | CHLPS 43 kDa Protein Homolog_4 | ||
| 1045 | Conserved Hypothetical Membrane Protein | ||
| 0251 | Conserved Hypothetical Protein | ||
| 0278 | Conserved Outer Membrane Lipoprotein Protein | ||
| 0907 | CutA-like Periplasmic Divalent Cation Tolerance Protein | ||
| 0171 | gusA | GMP Synthase | |
| 0172 | gusB | Inosine 5'-Monophosphase Dehydrogenase | |
| 0608 | Uridine 5'-Monophosphate Synthase | ||
| 0735 | Uridine Kinase | ||
| 0980 | Similar to Saccharomyces cerevisiae 52.9 KDa Protein | ||
| 0232 | Similarity to 5'-Methylthioadenosine Nucleosidase | ||
| 1046 | Tryptophan Hydroxylase | ||
| 0477 | yqeV_Bs | Conserved Hypothetical Protein | |
| 0048 | yqfF-Bs | Conserved Hypothetical IM Protein | |
| 0587 | yvyD_Bs | Conserved Hypothetical Protein | |
| 0143 | yxjG_Bs_1 | Conserved Hypothetical Protein | |
| 0448 | yxjG_Bs_2 | Conserved Hypothetical Protein | |
| 0006 | |||
| 0007 | |||
| 0008 | |||
| 0009 | |||
| 0010 | |||
| 0011 | |||
| 0012 | |||
| 0028 | |||
| 0029 | |||
| 0034 | |||
| 0041 | |||
| 0042 | |||
| 0043 | |||
| 0044 | |||
| 0045 | |||
| 0046 | |||
| 0047 | |||
| 0049 | |||
| 0050 | |||
| 0051 | |||
| 0063 | |||
| 0064 | |||
| 0066 | |||
| 0067 | |||
| 0069 | |||
| 0070 | |||
| 0099 | |||
| 0124 | |||
| 0125 | |||
| 0126 | |||
| 0130 | |||
| 0131 | |||
| 0132 | |||
| 0142 | |||
| 0146 | |||
| 0147 | |||
| 0155 | |||
| 0156 | |||
| 0157 | |||
| 0158 | |||
| 0159 | |||
| 0162 | |||
| 0163 | |||
| 0164 | |||
| 0165 | |||
| 0166 | |||
| 0167 | |||
| 0168 | |||
| 0169 | |||
| 0170 | |||
| 0173 | |||
| 0174 | |||
| 0175 | |||
| 0177 | |||
| 0178 | |||
| 0179 | |||
| 0180 | |||
| 0181 | |||
| 0190 | |||
| 0203 | |||
| 0204 | |||
| 0205 | |||
| 0209 | |||
| 0210 | |||
| 0211 | |||
| 0212 | |||
| 0213 | |||
| 0214 | |||
| 0215 | |||
| 0216 | |||
| 0218 | |||
| 0220 | |||
| 0221 | |||
| 0222 | |||
| 0223 | |||
| 0224 | |||
| 0225 | |||
| 0226 | |||
| 0233 | |||
| 0240 | |||
| 0241 | |||
| 0242 | |||
| 0243 | |||
| 0266 | |||
| 0267 | |||
| 0268 | |||
| 0277 | |||
| 0283 | |||
| 0284 | |||
| 0285 | |||
| 0287 | |||
| 0352 | |||
| 0353 | |||
| 0354 | |||
| 0355 | |||
| 0356 | |||
| 0357 | |||
| 0358 | |||
| 0365 | |||
| 0366 | |||
| 0367 | |||
| 0368 | |||
| 0371 | |||
| 0372 | |||
| 0375 | |||
| 0376 | |||
| 0391 | |||
| 0398 | |||
| 0404 | |||
| 0431 | |||
| 0432 | |||
| 0439 | |||
| 0440 | |||
| 0455 | |||
| 0456 | |||
| 0457 | |||
| 0458 | |||
| 0459 | |||
| 0460 | |||
| 0461 | |||
| 0462 | |||
| 0463 | |||
| 0464 | |||
| 0465 | |||
| 0472 | |||
| 0473 | |||
| 0481 | |||
| 0483 | |||
| 0492 | |||
| 0493 | |||
| 0494 | |||
| 0498 | |||
| 0499 | |||
| 0516 | |||
| 0517 | |||
| 0523 | |||
| 0524 | |||
| 0553 | |||
| 0574 | |||
| 0600 | |||
| 0656 | |||
| 0664 | |||
| 0677 | |||
| 0678 | |||
| 0685 | |||
| 0686 | |||
| 0724 | |||
| 0731 | |||
| 0745 | |||
| 0753 | |||
| 0794 | |||
| 0795 | |||
| 0796 | |||
| 0797 | |||
| 0798 | |||
| 0799 | |||
| 0829 | |||
| 0830 | |||
| 0831 | |||
| 0881 | |||
| 0882 | |||
| 0913 | |||
| 0914 | |||
| 0930 | |||
| 0944 | |||
| 0964 | |||
| 0975 | |||
| 0976 | |||
| 0977 | |||
| 0978 | |||
| 1018 | |||
| 1023 | |||
| 1027 | |||
| 1029 | |||
| 1040 | |||
| 1051 | |||
| 1052 | |||
| 1053 | |||
| 1054 | |||
| 1055 | |||
| 1056 | |||
| 1064 | |||
| 1065 | |||
| 1066 | |||
| 1070 | |||
| 1071 | |||
| 1072 | |||
| tRNAs | ||||
| tRNA # | Begin | End | Type | Codon |
| 1 | 89657 | 89728 | Thr | GGT |
| 2 | 90998 | 91070 | Trp | CCA |
| 3 | 199301 | 199229 | Met | CAT |
| 4 | 199390 | 199317 | Met | CAT |
| 5 | 296075 | 296147 | Val | TAC |
| 6 | 296151 | 296224 | Asp | GTC |
| 7 | 409848 | 409922 | Pro | TGG |
| 8 | 462141 | 462214 | Arg | CCT |
| 9 | 672236 | 672318 | Leu | CAA |
| 10 | 677264 | 677337 | Arg | TCG |
| 11 | 739403 | 739486 | Leu | CAG |
| 12 | 781610 | 781680 | Gly | TCC |
| 13 | 784822 | 784896 | Glu | TTC |
| 14 | 784922 | 784994 | Lys | TTT |
| 15 | 836119 | 836191 | Ala | GGC |
| 16 | 843926 | 843999 | Pro | GGG |
| 17 | 877400 | 877473 | Arg | ACG |
| 18 | 1085605 | 1085676 | Gln | TTG |
| 19 | 1142034 | 1142118 | Ser | TGA |
| 20 | 1175863 | 1175944 | Leu | TAG |
| 21 | 1230028 | 1229942 | Ser | CGA |
| 22 | 1137462 | 1137389 | Val | GAC |
| 23 | 1030603 | 1030533 | Cys | GCA |
| 24 | 1000022 | 999949 | His | GTG |
| 25 | 961607 | 961536 | Gly | GCC |
| 26 | 807413 | 807341 | Arg | TCT |
| 27 | 786780 | 786708 | Thr | CGT |
| 28 | 715971 | 715889 | Leu | TAA |
| 29 | 708441 | 708354 | Ser | GCT |
| 30 | 680259 | 680178 | Leu | GAG |
| 31 | 631445 | 631373 | Phe | GAA |
| 32 | 626987 | 626901 | Ser | GGA |
| 33 | 293477 | 293405 | Thr | TGT |
| 34 | 293399 | 293317 | Tyr | GTA |
| 35 | 269142 | 269070 | Ala | TGC |
| 36 | 269065 | 268992 | Ile | GAT |
| 37 | 1643089 | 164318 | Asn | GTT |
| 38 | 87522 | 87450 | Met | CAT |
Davis, Ronald, Stephens, Richard S., Kalman, Sue S., Mitchell, Wayne
| Patent | Priority | Assignee | Title |
| 10188722, | Sep 18 2008 | Aviex Technologies LLC | Live bacterial vaccines resistant to carbon dioxide (CO2), acidic pH and/or osmolarity for viral infection prophylaxis or treatment |
| 10596247, | Feb 20 2015 | Board of Regents, The University of Texas System | Methods and compositions for attenuated chlamydia as vaccine and vector |
| 10627409, | Jan 14 2011 | The Regents of the University of California | Therapeutic antibodies against ROR-1 protein and methods for use of same |
| 10689425, | Mar 27 2008 | Purdue Research Foundation | Collagen-binding synthetic peptidoglycans, preparation, and methods of use |
| 10745447, | Sep 28 2015 | UNIVERSITY OF FLORIDA RESEARCH FOUNDATION, INC | Methods and compositions for antibody-evading virus vectors |
| 10772931, | Apr 25 2014 | Purdue Research Foundation | Collagen binding synthetic peptidoglycans for treatment of endothelial dysfunction |
| 10900973, | Jan 14 2011 | The Regents of the University of California | Therapeutic antibodies against ROR-1 protein and methods for use of same |
| 10907176, | Jan 14 2015 | The University of North Carolina at Chapel Hill | Methods and compositions for targeted gene transfer |
| 11129906, | Dec 07 2016 | Chimeric protein toxins for expression by therapeutic bacteria | |
| 11180535, | Dec 07 2016 | Saccharide binding, tumor penetration, and cytotoxic antitumor chimeric peptides from therapeutic bacteria | |
| 11208438, | Sep 28 2015 | The University of North Carolina at Chapel Hill; University of Florida Research Foundation, Inc. | Methods and compositions for antibody-evading virus vectors |
| 11529424, | Jul 07 2017 | SYMIC HOLDINGS, INC | Synthetic bioconjugates |
| 11536727, | Jan 14 2011 | The Regents of the University of California | Therapeutic antibodies against ROR-1 protein and methods for use of same |
| 11840555, | Sep 28 2015 | The University of North Carolina at Chapel Hill; University of Florida Research Foundation, Inc. | Methods and compositions for antibody-evading virus vectors |
| 11905523, | Oct 17 2019 | GINKGO BIOWORKS, INC | Adeno-associated viral vectors for treatment of Niemann-Pick Disease type-C |
| 11976096, | Apr 03 2018 | Ginkgo Bioworks, Inc. | Antibody-evading virus vectors |
| 11981914, | Mar 21 2019 | Ginkgo Bioworks, Inc. | Recombinant adeno-associated virus vectors |
| 12060390, | Apr 03 2018 | Ginkgo Bioworks, Inc. | Antibody-evading virus vectors |
| 12091435, | Apr 03 2018 | GINKGO BIOWORKS, INC | Antibody-evading virus vectors |
| 12104163, | Aug 19 2020 | Sarepta Therapeutics, Inc | Adeno-associated virus vectors for treatment of Rett syndrome |
| 12116384, | Apr 03 2018 | GINKGO BIOWORKS, INC | Virus vectors for targeting ophthalmic tissues |
| 6992358, | Dec 05 2003 | Kabushiki Kaisha Toshiba | Semiconductor device and method for manufacturing the same |
| 7081245, | Apr 04 2000 | sanofi pasteur limited | Chlamydia antigens and corresponding DNA fragments and uses thereof |
| 7183402, | Mar 12 1999 | sanofi pasteur limited | Chlamydia antigens and corresponding DNA fragments and uses thereof |
| 7285276, | Mar 12 1999 | sanofi pasteur limited | Chlamydia antigens and corresponding DNA fragments and uses thereof |
| 7297341, | Dec 23 1998 | sanofi pasteur limited | Chlamydia antigens and corresponding DNA fragments and uses thereof |
| 7314869, | Sep 20 1999 | sanofi pasteur limited | Chlamydia antigens and corresponding DNA fragments and uses thereof |
| 7326545, | Dec 01 1998 | sanofi pasteur limited | Chlamydia antigens and corresponding DNA fragments and uses thereof |
| 7335370, | Dec 28 1998 | sanofi pasteur limited | Chlamydia antigens and corresponding DNA fragments and uses thereof |
| 7553493, | Oct 01 2001 | sanofi pasteur limited | Chlamydia flagellar protein antigen |
| 7595058, | May 03 1999 | sanofi pasteur limited | Chlamydia antigens and vaccine uses of the protein |
| 7629327, | Mar 12 1999 | sanofi pasteur limited | Chlamydia 60 Kda CRMP antigens and vaccine uses |
| 7658934, | May 03 1999 | sanofi pasteur limited | Chlamydia antigens and protein vaccine |
| 7662391, | Sep 20 1999 | sanofi pasteur limited | Chlamydia outer membrane protein (OMP) and vaccine uses of the protein |
| 7736873, | Dec 01 1998 | sanofi pasteur limited | Chlamydia polypeptides and corresponding DNA fragments and uses thereof |
| 7754228, | Feb 13 2002 | Novartis Vaccines and Diagnostics, SRL | Cytotoxic T-cell epitopes from Chlamydia |
| 7850980, | Oct 01 2001 | sanofi pasteur limited | Chlamydia OMP antigen |
| 8092812, | Oct 01 2007 | Board of Regents, The University of Texas System | Methods and compositions for immunization against chlamydial infection and disease |
| 8114401, | Dec 18 1998 | Chlamydia trachomatis antigens | |
| 8435533, | Dec 15 2000 | Auburn University; Board of Regents, The University of Texas System | Methods and compositions for vaccination comprising nucleic acid and/or polypeptide sequences of Chlamydia |
| 8440208, | May 01 2007 | Board of Regents, The University of Texas System | Chlamydial antigens as reagents for diagnosis and treatment of chlamydial infection and disease |
| 9068007, | Oct 09 2008 | Board of Regents, The University of Texas System | Methods and compositions for chlamydial antigens for diagnosis and treatment of chlamydial infection and disease |
| 9200039, | Mar 15 2013 | SYMIC IP, LLC | Extracellular matrix-binding synthetic peptidoglycans |
| 9217016, | May 24 2011 | SYMIC OA CO | Hyaluronic acid-binding synthetic peptidoglycans, preparation, and methods of use |
| 9512192, | Mar 27 2008 | Purdue Research Foundation | Collagen-binding synthetic peptidoglycans, preparation, and methods of use |
| 9523695, | Jan 14 2011 | The Regents of the University of California | Therapeutic antibodies against ROR-1 protein and methods for use of same |
| 9872887, | Mar 15 2013 | Purdue Research Foundation | Extracellular matrix-binding synthetic peptidoglycans |
| 9933434, | Jan 14 2011 | The Regents of the University of California | Therapeutic antibodies against ROR-1 protein and methods for use of same |
| Patent | Priority | Assignee | Title |
| WO9927105, |
| Executed on | Assignor | Assignee | Conveyance | Frame | Reel | Doc |
| Nov 11 1999 | The Regents of the University of California | (assignment on the face of the patent) | ||||
| Sep 14 2000 | STEPHENS, RICHARD S | The Regents of the University of California | ASSIGNMENT OF ASSIGNORS INTEREST SEE DOCUMENT FOR DETAILS | 014834 | 0739 | |
| Sep 14 2000 | MITCHELL, WAYNE | The Regents of the University of California | ASSIGNMENT OF ASSIGNORS INTEREST SEE DOCUMENT FOR DETAILS | 014834 | 0739 | |
| Sep 18 2000 | KALMAN, SUE S | The Regents of the University of California | ASSIGNMENT OF ASSIGNORS INTEREST SEE DOCUMENT FOR DETAILS | 014834 | 0739 | |
| Sep 18 2000 | DAVIS, RONALD W | The Regents of the University of California | ASSIGNMENT OF ASSIGNORS INTEREST SEE DOCUMENT FOR DETAILS | 014834 | 0739 | |
| Mar 19 2009 | UNIVERSITY OF CALIFORNIA BERKELEY | NATIONAL INSTITUTES OF HEALTH NIH , U S DEPT OF HEALTH AND HUMAN SERVICES DHHS , U S GOVERNMENT | CONFIRMATORY LICENSE SEE DOCUMENT FOR DETAILS | 022416 | 0629 | |
| Jun 23 2017 | University of California | NIH | CONFIRMATORY LICENSE SEE DOCUMENT FOR DETAILS | 042800 | 0536 |
| Date | Maintenance Fee Events |
| Dec 28 2004 | ASPN: Payor Number Assigned. |
| Jan 22 2008 | LTOS: Pat Holder Claims Small Entity Status. |
| May 23 2008 | M2551: Payment of Maintenance Fee, 4th Yr, Small Entity. |
| May 23 2012 | M2552: Payment of Maintenance Fee, 8th Yr, Small Entity. |
| Jul 01 2016 | REM: Maintenance Fee Reminder Mailed. |
| Nov 23 2016 | EXP: Patent Expired for Failure to Pay Maintenance Fees. |
| Date | Maintenance Schedule |
| Nov 23 2007 | 4 years fee payment window open |
| May 23 2008 | 6 months grace period start (w surcharge) |
| Nov 23 2008 | patent expiry (for year 4) |
| Nov 23 2010 | 2 years to revive unintentionally abandoned end. (for year 4) |
| Nov 23 2011 | 8 years fee payment window open |
| May 23 2012 | 6 months grace period start (w surcharge) |
| Nov 23 2012 | patent expiry (for year 8) |
| Nov 23 2014 | 2 years to revive unintentionally abandoned end. (for year 8) |
| Nov 23 2015 | 12 years fee payment window open |
| May 23 2016 | 6 months grace period start (w surcharge) |
| Nov 23 2016 | patent expiry (for year 12) |
| Nov 23 2018 | 2 years to revive unintentionally abandoned end. (for year 12) |